We highlight applications of first-principles calculations based on density-functional theory, density-functional perturbation theory and molecular dynamics. We present intuitively the background of the various calculations. We exemplify with investigations of the physical behavior of major planetary materials under extreme conditions, currently unreachable in experiments: the phase diagram of the (Fe,Mg)SiO3 perovskite and post-perovskite system; the phase diagram of H2O ice; the electrical conductivity of iron in planetary cores. We briefly present the WURM project on theoretical mineral spectroscopy as a model for sharing numerical data obtained by mineral physicists with planetary scientists interested in surface mineralogy.

We investigate the X-ray photoelectron spectroscopy (XPS) binding energies of As 3d in Si for various defects in neutral and charged states by first-principles calculation. It is found that the complexes of a substitutional As and a vacancy in charged and neutral states explain the experimentally observed unknown peak very well.

Based on first-principles calculations, we present a quantum confinement mechanism for the band gaps of blue phosphorene nanoribbons (BPNRs) as a function of their widths. The BPNRs considered have either armchair or zigzag shaped edges on both sides with hydrogen saturation. Both the two types of nanoribbons are shown to be indirect semiconductors. An enhanced energy gap of around 1 eV can be realized when the ribbon's width decreases to ˜10 Å. The underlying physics is ascribed to the quantum confinement effect. More importantly, the parameters to describe quantum confinement are obtained by fitting the calculated band gaps with respect to their widths. The results show that the quantum confinement in armchair nanoribbons is stronger than that in zigzag ones. This study provides an efficient approach to tune the band gap in BPNRs.

We investigate the impact of water, a polar solvent, on the optical absorption of prototypical silicon clusters with oxygen passivation. We approach this complex problem by assessing the contributions of three factors: chemical reactivity; thermal equilibration and dielectric screening. We find that the silanone (Si=O) functional group is not chemically stable in the presence of water and exclude this as a source of significant red shift in absorption in aqueous environments. We perform firstprinciples molecular dynamics simulations of the solvation of an oxygenated silicon cluster with explicit water molecules at 300 K. We find a systematic 0.7 eV red shift in the absorption gap of this cluster, which we attribute to thermal strain of the molecular structure. Surprisingly, we find no observable screening impact of the solvent, in contrast with consistent blue shifts observed for similarly sized organic molecules in polar solvents. The predicted red shift is expected to be significantly smaller for larger Si quantum dots produced experimentally, guaranteeing that their vacuum optical properties are preserved even in aqueous environments.

The electronic structures of ABO3 ferroelectrics are calculated within the density functional theory, and their evolution is analyzed as the crystal-field symmetry changes from cubic to rhombohedral via tetragonal phases. Electronic structure fingerprints that characterize each phase from their electronic spectra are identified. We carried out electron-energy loss spectroscopy experiments by using synchrotron radiation and compared these results to the theoretical spectra calculated within DFT-LDA. The dominant role of the BO6 octahedra in the formation of the energy spectra of ABO3 compounds was demonstrated. Anomalous behavior of plasmons in ferroelectrics was exhibited by the function representing the characteristic energy loss in the region of phase transition.

We have investigated the initial stage of hydrolysis process of Ga-terminated GaN surfaces by using first-principlestheoretical calculations. We found that the activation barrier of H2O dissociation at the kinked site of the Ga-terminated GaN surface is about 0.8 eV, which is significantly lower than that at the stepped site of about 1.2 eV. This is consistent with the experimental observation where a step-terrace structure is observed after the etching process of Ga-terminated GaN surfaces with catalyst-referred etching method. Detailed analysis on the nature of the chemical interaction uring the hydrolysis processes will be discussed. PMID:23679914

The ability of nonlinear electronic spectroscopy to track folding/unfolding processes of proteins in solution by monitoring aromatic interactions is investigated by first-principles simulations of two-dimensional (2D) electronic spectra of a model peptide. A dominant reaction pathway approach is employed to determine the unfolding pathway of a tetrapeptide, which connects the initial folded configuration with stacked aromatic side chains and the final unfolded state with distant noninteracting aromatic residues. The ?-stacking and excitonic coupling effects are included through ab initio simulations based on multiconfigurational methods within a hybrid quantum mechanics/molecular mechanics scheme. It is shown that linear absorption spectroscopy in the ultraviolet (UV) region is unable to resolve the unstacking dynamics characterized by the three-step process: T-shaped?twisted offset stacking?unstacking. Conversely, pump-probe spectroscopy can be used to resolve aromatic interactions by probing in the visible region, the excited-state absorptions (ESAs) that involve charge-transfer states. 2D?UV spectroscopy offers the highest sensitivity to the unfolding process, by providing the disentanglement of ESA signals belonging to different aromatic chromophores and high correlation between the conformational dynamics and the quartic splitting. PMID:25145908

We perform first-principles computational tensile and compressive tests (FPCTT and FPCCT) to investigate the intrinsic bonding and mechanical properties of a ?-TiAl intermetallic compound (L 1(0) structure) using a first-principles total energy method. We found that the stress-strain relations and the corresponding theoretical tensile strengths exhibit strong anisotropy in the [001], [100] and [110] crystalline directions, originating from the structural anisotropy of ?-TiAl. Thus, ?-TiAl is a representative intermetallic compound that includes three totally different stress-strain modes. We demonstrate that all the structure transitions in the FPCTT and FPCCT result from the breakage or formation of bonds, and this can be generalized to all the structural transitions. Furthermore, based on the calculations we qualitatively show that the Ti-Al bond should be stronger than the Ti-Ti bond in ?-TiAl. Our results provide a useful reference for understanding the intrinsic bonding and mechanical properties of ?-TiAl as a high-temperature structural material. PMID:21825422

Oxidation state is a powerful concept that is widely used in chemistry and materials physics, although the concept itself is arguably ill-defined quantum mechanically. In this work, we present impartial comparison of four, well-recognized theoretical approaches based on Lowdin atomic orbital projection, Bader decomposition, maximally localized Wannier function, and occupation matrix diagonalization, for assessing how well transition metal oxidation states can be characterized. Here, we study a representative molecular complex, tris(bipyridine)ruthenium. We also consider the influence of water solvation through first-principles molecular dynamics as well as the improved electronic structure description for strongly correlated d-electrons by including Hubbard correction in density functional theory calculations.

We carried out a comprehensive study on the B1s core-level X-ray photoelectron spectroscopy (XPS) binding energies for B clusters in crystalline Si using a first-principles calculation with careful evaluation of the local potential boundary condition for the model system, where convergence within 0.1 eV was confirmed for the supercell size. For ion-implanted samples, we identified experimental peaks due to B clusters and threefold B as icosahedral B{sub 12} and <001>B-Si defects, respectively. For as-doped samples prepared by plasma doping, it was found that the calculated XPS binding energies for complexes of vacancies and B atoms were consistent with the experimental spectra.

Silicon and aluminium chemical environments in silicate and aluminosilicate glasses with compositions 60SiO2·20Na2O·20CaO (CSN), 60SiO2·20Al2O3·20CaO (CAS), 78SiO2·11Al2O3·11Na2O (NAS) and 60SiO2·10Al2O3·10Na2O·20CaO (CASN) have been investigated by 27Al and 29Si solid state magic angle spinning (MAS) and multiple quantum MAS (MQMAS) nuclear magnetic resonance (NMR) experiments. To interpret the NMR data, first-principles calculations using density functional theory were performed on structural models of these glasses. These models were generated by Shell-model molecular dynamics (MD) simulations. The theoretical NMR parameters and spectra were computed using the gauge including projected augmented wave (GIPAW) method and spin-effective Hamiltonians, respectively. This synergetic computational-experimental approach offers a clear structural characterization of these glasses, particularly in terms of network polymerization, chemical disorder (i.e. Si and Al distribution in second coordination sphere) and modifier cation distributions. The relationships between the local structural environments and the 29Si and 27Al NMR parameters are highlighted, and show that: (i) the isotropic chemical shift of both 29Si and 27Al increases of about +5 ppm for each Al added in the second sphere and (ii) both the 27Al and 29Si isotropic chemical shifts linearly decrease with the reduction of the average Si/Al-O-T bond angle. Conversely, 27Al and 29Si NMR parameters are much less sensitive to the connectivity with triple bridging oxygen atoms, precluding their indirect detection from 27Al and 29Si NMR.

Aqueous fluids play an essential role in mass and energy transfer in the lithosphere. Their presence has also a large effect on physical properties of rocks, e.g. the electrical conductivity. Many chemical and physical properties of aqueous fluids strongly depend on the speciation, but very little is known about this fundamental parameter at high pressures and temperatures, e.g. at subduction zone conditions. Here we use a combined approach of first-principles molecular dynamics simulation and Raman spectroscopy to study the molecular structure of aqueous 2~mol/kg MgSO4 fluids up to pressures of 3~GPa and temperatures of 750~°C. MgSO4-H2O is selected as a model system for sulfate bearing subduction zone fluids. The simulations are performed using Car-Parrinello dynamics, a system size of 120 water and four MgSO4 molecules with production runs of at least 10~ps at each P and T. Raman spectra were obtained in situ using a Bassett-type hydrothermal diamond anvil cell with external heating. Both simulation and spectroscopic data show a dynamic co-existence of various associated molecular species as well as dissociated Mg2+ and SO42- in the single phase fluid. Fitting the Raman signal in the frequency range of the ?1-SO42- stretching mode yields the P-T dependence of the relative proportions of different peaks. The latter can be assigned to species based on literature data and related to the species found in the simulation. The dominant associated species found in the P-T range of interest here are Mg-SO4 ion pairs with one (monodentate) and two (bidentate) binding sites. At the highest P and T, an additional peak is identified. At low pressures and high temperature (T>230~°C), kieserite, MgSO4·H2O, nucleated in the experiment. At the same conditions the simulations show a clustering of Mg, which is interpreted as a precursor of precipitation. In conclusion, the speciation of aqueous MgSO4 fluid shows a complex behavior at high P and T that cannot be extrapolated from ambient conditions. The combination of molecular modeling and in situ spectroscopic experiments is a promising approach towards quantitative understanding of geochemical processes in subduction zones.

A DFT-based molecular model for imidazolium-silica-based nanoparticle networks (INNs) is presented. The INNs were synthesized and characterized by using small-angle X-ray scattering (SAXS), NMR spectroscopy, and theoretical ab initio calculations. (11) B and (31) P HETCOR CP MAS experiments were recorded. Calculated (19) F?NMR spectroscopy results, combined with the calculated anion-imidazolium (IM) distances, predicted the IM chain density in the INN, which was also confirmed from thermogravimetric analysis/mass spectrometry results. The presence of water molecules trapped between the nanoparticles is also suggested. First considerations on possible ?-? stacking between the IM rings are presented. The predicted electronic properties confirm the photoluminescence emissions in the correct spectral domain. PMID:25241702

Firstprinciples density functional theory calculations were carried out to investigate the adsorption and oxidation of CO on the positively charged (101) surface of anatase, as well as the desorption of CO{sub 2} from it. We find that the energy gain on adsorption covers the activation energy required for the oxidation, while the energy gain on the latter is sufficient for the desorption of CO{sub 2}, leaving an oxygen vacancy behind. Molecular dynamics simulations indicate that the process can be spontaneous at room temperature. The oxidation process described here happens only in the presence of the hole. The possibility of a photocatalytic cycle is discussed assuming electron scavenging by oxygen.

The electronic structures of SmScO{sub 3}, GdScO{sub 3}, and DyScO{sub 3} are investigated by means of x-ray photoelectron spectroscopy, x-ray emission spectroscopy (XES), and x-ray absorption spectroscopy (XAS). A strong hybridization between Sc 3d and O 2p is found, and a contribution of the rare-earth 5d states to this hybridization is not excluded. The band gaps of the compounds are determined by combining XES and XAS measurements. For SmScO{sub 3}, GdScO{sub 3}, and DyScO{sub 3} the band gaps were determined to be 5.6, 5.8, and 5.9 eV, respectively. Magnetization versus temperature measurements reveal antiferromagnetic coupling at 2.96 (SmScO{sub 3}), 2.61 (GdScO{sub 3}), and 3.10 K (DyScO{sub 3}). For DyScO{sub 3} a Rietveld refinement of a 2 K neutron-diffraction data set gives the spin arrangement of Dy in the Pbnm structure (Shubnikov group: Pb{sup '}n{sup '}m{sup '})

Present quantum Monte Carlo codes use statistical techniques adapted to find the amplitude of a quantum system or the associated eigenvalues. Thus, they do not use a true physical random source. It is demonstrated that, in fact, quantum probability admits a description based on a specific class of random process at least for the single particle case. Then a firstprinciple Monte Carlo code that exactly simulates quantum dynamics can be constructed. The subtle question concerning how to map random choices in amplitude interferences is explained. Possible advantages of this code in simulating single hit experiments are discussed.

We have theoretically investigated the dielectric properties of fluorite CeO2 as well as hexagonal and cubic Ce2O3 by using first-principles pseudopotentials techniques within the local density approximation. Calculated electronic and lattice dielectric constants of CeO2 are in good agreement with previous theoretical and experimental results. For Ce2O3, the hexagonal phase has a lattice dielectric constant comparable to that of CeO2,

This paper is intended to challenge systems professionals to think about systems -- not at the process level but at the foundational level: firstprinciples. System principles at the concept level, and what one understands about them, determine what one p...

Transversity observables, such as the T-odd Sivers single-spin asymmetry measured in deep inelastic lepton scattering on polarized protons and the distributions which are measured in deeply virtual Compton scattering, provide important constraints on the fundamental quark and gluon structure of the proton. In this talk I discuss the challenge of computing these observables from firstprinciples; i.e.; quantum chromodynamics, itself. A key step is the determination of the frame-independent light-front wavefunctions (LFWFs) of hadrons - the QCD eigensolutions which are analogs of the Schroedinger wavefunctions of atomic physics. The lensing effects of initial-state and final-state interactions, acting on LFWFs with different orbital angular momentum, lead to T-odd transversity observables such as the Sivers, Collins, and Boer-Mulders distributions. The lensing effect also leads to leading-twist phenomena which break leading-twist factorization such as the breakdown of the Lam-Tung relation in Drell-Yan reactions. A similar rescattering mechanism also leads to diffractive deep inelastic scattering, as well as nuclear shadowing and non-universal antishadowing. It is thus important to distinguish 'static' structure functions, the probability distributions computed the target hadron's light-front wavefunctions, versus 'dynamical' structure functions which include the effects of initial- and final-state rescattering. I also discuss related effects such as the J = 0 fixed pole contribution which appears in the real part of the virtual Compton amplitude. AdS/QCD, together with 'Light-Front Holography', provides a simple Lorentz-invariant color-confining approximation to QCD which is successful in accounting for light-quark meson and baryon spectroscopy as well as hadronic LFWFs.

Gersten has shown how Maxwell equations can be derived from firstprinciples, similar to those which have been used to obtain the Dirac relativistic electron equation. We show how Proca equations can be also deduced from firstprinciples, similar to those which have been used to find Dirac and Maxwell equations. Contrary to Maxwell equations, it is necessary to introduce a potential in order to transform a second order differential equation, as the Klein-Gordon equation, into a first order differential equation, like Proca equations.

Describes an evaluation of Web-based instruction at the University of Houston-Clear Lake (Texas) that showed that the design team had been distracted from many firstprinciples of instructional design by the creative chaos on the Web and discusses how self-reflection and role definitions allowed the team to overcome these disappointments and…

This paper is intended to challenge systems professionals to think about systems -- not at the process level but at the foundational level: firstprinciples. System principles at the concept level, and what one understands about them, determine what one practices at the process level -- that is, how one defines systems engineering''. When Kant, Kepler, Newton, Einstein, and the

This paper is intended to challenge systems professionals to think about systems -- not at the process level but at the foundational level: firstprinciples. System principles at the concept level, and what one understands about them, determine what one practices at the process level -- that is, how one defines ``systems engineering``. When Kant, Kepler, Newton, Einstein, and the

We have done theoretical calculations and simulations for infrared spectroscopy at the MMT 6.5 m with laser guide star AO, which provides almost full sky coverage. The results show we can expect 40-60% of the photons from a unresolved source within 0.2 arcsec diameter circle for J, H, K, L and M bands under typical atmospheric seeing condition at 2.2 micron. Therefore, the spectrograph entrance slit size should match the 0.2 arcsec image to obtain high throughput. Higher resolution can be achieved by narrowing down the slit size to match the diffraction-limited image core size of about 0.1 arcsec in the infrared. However, the throughput will be correspondingly reduced by a factor of two. Due to the limited atmospheric isoplanatic angle in the J, H and K bands, the encircled photon percentage within 0.2 arcsec diameter drops from 40-60% when the object is at the laser pointing direction to 20-40% when the object is about 30 arcsec away from the laser direction. Therefore, the useful field of view for AO multiple object spectroscopy is about 60 arcsec. Further studies of IR background (sky and thermal) and IR detector performance show that spectral resolution of R = 2,000 can take full advantage of AO images without much penalty due to the dark current of the IR detector and IR OH sky emission lines. We have also studied natural guide star AO spectroscopy. More details are in the paper.

We present a firstprinciples method for calculating positron lifetimes in solids, based on self-consistent calculations using the Linear Muffin-Tin Orbital method. Local density approximations are used for both electron-electron and electron-positron interactions. Results are presented for a variety of elemental metals and vacancies to demonstrate the reliability of this approach. Theoretical calculations of positron lifetimes can be used to interpret experimental data. As an examples of this, we interpret our experimental lifetime data for the oxide superconductor Ba{sub 1-x}K{sub x}BiO{sub 3} using calculations based on this method. 12 refs., 3 figs.

The purpose of this work is to predict elastic and thermodynamic properties of Cr-based alloys based on first-principles calculations. The ultimate goal is to develop new materials for hightemperature applications in energy systems. In this study, we choose both Poisson ratio and Rice–Thomson parameter as computational screening tool for identifying ductilizing additives to the refractory alloys. In this report, we present our preliminary results on bulk modulus and enthalpy of mixing of 25 bcc Cr15X1 alloys.

Firstprinciples calculations within the local-spin-density-functional theory (LSDFF) framework are presented of densities of electronic states for MnO, LiMnO{sub 2} in the monoclinic and orthorhombic structures, cubic LiMn{sub 2}O{sub 4} spinel and {lambda}-MnO{sub 2} (delithiated spinel), all in antiferromagnetic spin configurations. The changes in energy spectra as the Mn oxidation state varies between 2+ and 4+ are illustrated. Preliminary calculations for Co-doped LiMnO{sub 2} are presented, and the destabilization of a monoclinic relative to a rhombohedral structure is discussed.

In this thesis, theoretical models and computer simulations are employed to study several problems of single-molecule spectroscopy and vibrational spectroscopy in condensed phases. The first part of the thesis concentrates ...

The cores of Earth and other terrestrial planets are made up largely of iron1 and it is therefore very important to understand iron's physical properties. Chemical diffusion is one such property and is central to many processes, such as crystal growth, and viscosity. Debate still surrounds the explanation for the seismologically observed anisotropy of the inner core2, and hypotheses include convection3, anisotropic growth4 and dendritic growth5, all of which depend on diffusion. In addition to this, the main deformation mechanism at the inner-outer core boundary is believed to be diffusion creep6. It is clear, therefore, that to gain a comprehensive understanding of the core, a thorough understanding of diffusion is necessary. The extremely high pressures and temperatures of the Earth's core make experiments at these conditions a challenge. Low-temperature and low-pressure experimental data must be extrapolated across a very wide gap to reach the relevant conditions, resulting in very poorly constrained values for diffusivity and viscosity. In addition to these dangers of extrapolation, preliminary results show that magnetisation plays a major role in the activation energies for diffusion at low pressures therefore creating a break down in homologous scaling to high pressures. Firstprinciples calculations provide a means of investigating diffusivity at core conditions, have already been shown to be in very good agreement with experiments7, and will certainly provide a better estimate for diffusivity than extrapolation. Here, we present firstprinciples simulations of self-diffusion in solid iron for the FCC, BCC and HCP structures at core conditions in addition to low-temperature and low-pressure calculations relevant to experimental data. 1. Birch, F. Density and composition of mantle and core. Journal of Geophysical Research 69, 4377-4388 (1964). 2. Irving, J. C. E. & Deuss, A. Hemispherical structure in inner core velocity anisotropy. Journal of Geophysical Research 116, B04307 (2011). 3. Buffett, B. A. Onset and orientation of convection in the inner core. Geophysical Journal International 179, 711-719 (2009). 4. Bergman, M. Measurements of electric anisotropy due to solidification texturing and the implications for the Earth's inner core. Nature 389, 60-63 (1997). 5. Deguen, R. & Cardin, P. Thermochemical convection in Earth's inner core. Geophysical Journal International 187, 1101-1118 (2011). 6. Reaman, D. M., Daehn, G. S. & Panero, W. R. Predictive mechanism for anisotropy development in the Earth's inner core. Earth and Planetary Science Letters 312, 437-442 (2011). 7. Ammann, M. W., Brodholt, J. P., Wookey, J. & Dobson, D. P. First-principles constraints on diffusion in lower-mantle minerals and a weak D'' layer. Nature 465, 462-5 (2010).

A method of calculating inductances based on firstprinciples is presented, which has the advantage over the more popular simulators in that fundamental formulas are explicitly used so that a deeper understanding of the inductance calculation is obtained with no need for explicit discretization of the inductor. It also has the advantage over the traditional method of formulas or table lookups in that it can be used for a wider range of configurations. It relies on the use of fast computers with a sophisticated mathematical computing language such as Mathematica to perform the required integration numerically so that the researcher can focus on the physics of the inductance calculation and not on the numerical integration. PMID:25402467

The reaction dynamics of excited electronic states in nucleic acid bases is a key process in DNA photodamage. Recent ultrafast spectroscopy experiments have shown multi-component decays of excited uracil and thymine, tentatively assigned to nonadiabatic transitions involving multiple electronic states. Using both quantum chemistry and firstprinciples quantum molecular dynamics methods we show that a true minimum on the bright S{sub 2} electronic state is responsible for the first step which occurs on a femtosecond timescale. Thus the observed femtosecond decay does not correspond to surface crossing as previously thought. We suggest that subsequent barrier crossing to the minimal energy S{sub 2}/S{sub 1} conical intersection is responsible for the picosecond decay.

Graphene has recently attracted intensive attentions owing to its remarkable structural and electronic properties and its significant potential for applications in electronic and optoelectronic devices for size miniaturization and fast electron transportation. However, bulk graphene is a semi-metal with zero bandgap Eg, and opening a sizable Eg is critical for building operational graphene-based transistors. Recently, a new scheme of opening bandgap through punching nanoscale holes in graphene sheet, the graphene nanomesh, was proposed and verified experimentally [1]. However, the mechanism leading to the bandgap opening remains unknown. We have carried out first-principles calculations based on density functional theory (DFT) to study the bandgap opening mechanism and Eg as functions of structural parameters, including the hole size, the hole shape, and the hole-hole distances. Our results suggest that the bandgap opening is a result of quantum confinement at nanomesh necks, while the value of Eg depends not only on the width of nanomesh necks, but also on the chirality of the hole edge. This work was supported by the start-up research funds from Colorado School of Mines. [4pt] [1] J. Bai, X. Zhong, S. Jiang, Y. Huang, and X. Duan, Nature Nanotech. 5, 190 (2010).

Producing ab initio ro-vibrational energy levels of small, gas-phase molecules with an accuracy of 0.10 cm^{-1} would constitute a significant step forward in theoreticalspectroscopy and would place calculated line positions considerably closer to typical experimental accuracy. Such an accuracy has been recently achieved for the H_3^+ molecular ion for line positions up to 17 000 cm ^{-1}. However, since H_3^+ is a two-electron system, the electronic structure methods used in this study are not applicable to larger molecules. A major breakthrough was reported in ref., where an accuracy of 0.10 cm^{-1} was achieved ab initio for seven water isotopologues. Calculated vibrational and rotational energy levels up to 15 000 cm^{-1} and J=25 resulted in a standard deviation of 0.08 cm^{-1} with respect to accurate reference data. As far as line intensities are concerned, we have already achieved for water a typical accuracy of 1% which supersedes average experimental accuracy. Our results are being actively extended along two major directions. First, there are clear indications that our results for water can be improved to an accuracy of the order of 0.01 cm^{-1} by further, detailed ab initio studies. Such level of accuracy would already be competitive with experimental results in some situations. A second, major, direction of study is the extension of such a 0.1 cm^{-1} accuracy to molecules containg more electrons or more than one non-hydrogen atom, or both. As examples of such developments we will present new results for CO, HCN and H_2S, as well as preliminary results for NH_3 and CH_4. O.L. Polyansky, A. Alijah, N.F. Zobov, I.I. Mizus, R. Ovsyannikov, J. Tennyson, L. Lodi, T. Szidarovszky and A.G. Csaszar, Phil. Trans. Royal Soc. London A, {370}, 5014-5027 (2012). O.L. Polyansky, R.I. Ovsyannikov, A.A. Kyuberis, L. Lodi, J. Tennyson and N.F. Zobov, J. Phys. Chem. A, (in press). L. Lodi, J. Tennyson and O.L. Polyansky, J. Chem. Phys. {135}, 034113 (2011).

Firstprinciplestheoretical studies of dissociative adsorption of H{sub 2}, H{sub 2}O, SiH{sub 4} and other species on Si(100)-2x1 demonstrate some common principles that permit qualitative understanding of the mechanisms of reactive adsorption on Si. The structures of transition states and the interactions among surface sites can also be understood in terms of correlations between surface structure and local electron density. For example, the transition states for dissociative adsorption involve buckled surface dimers, which present both electrophilic and nucleophilic reaction sites and allow efficient addition across the dimer. A surface Diels-Alder reaction will also be described, in which symmetric addition to an unbuckled surface dimer is allowed by orbital symmetry. The Diets-Alder product establishes novel reactive surface sites that may be useful for subsequent surface modification. This work has been done in collaboration with Sharmila Pai, Robert Konecny and Anita Robinson Brown.

The properties of silicon dioxide have been studied extensively over the years. However, there still remain major unanswered questions regarding the nature of the optical spectrum and the role of excitonic effects in this technologically important material. In this work, we present an ab initio study of the optical absorption spectrum of alpha-quartz, using a newly developed first-principles method which includes self-energy and electron-hole interaction effects. The quasiparticle band structure is computed within the GW approximation to obtain a quantitative description of the single-particle excitations. The Bethe-Salpeter equation for the electron-hole excitations is solved to obtain the optical spectrum and to understand the spatial extent and physical properties of the excitons. The theoretical absorption spectrum is found to be in excellent agreement with the measured spectrum. We show that excitonic effects are crucial in the frequency range up to 5 eV above the absorption threshold.

Thorium-based materials are currently being investigated in relation with their potential utilization in Generation-IV reactors as nuclear fuels. One of the most important issues to be studied is their behavior under irradiation. A first approach to this goal is the study of point defects. By means of first-principles calculations within the framework of density functional theory, we study the stability and formation energies of vacancies, interstitials and Frenkel pairs in thorium carbide. We find that C isolated vacancies are the most likely defects, while C interstitials are energetically favored as compared to Th ones. These kind of results for ThC, to the best authors' knowledge, have not been obtained previously, neither experimentally, nor theoretically. For this reason, we compare with results on other compounds with the same NaCl-type structure.

We analyze the various crystalline phases of C observed upon exposing carbon nanotubes to H2 plasmas, which produces an amorphous carbon matrix with carbon nanocrystalls embedded in it. Structural characterization with electron diffraction and high-resolution TEM yields three distinct crystalline phases of C consistent with a fcc lattice with lattice parameter a = 4.25 å, a bcc lattice with a

First-principles calculations based on density functional theory are employed to study and predict the properties of boron and Mg boride nanostructures. For boron nanostructures, two-dimensional boron sheets are found to be metallic and made of mixtures of triangles and hexagons which benefit from the balance of two-center bonding and three-center bonding. This unusual bonding in boron sheets results in a self-doping picture where adding atoms to the hexagon centers does not change the number of bonding states but merely increases the electron count. Boron sheets can be either flat or buckled depending on the ratio between hexagons and triangles. Formed by stacking two identical boron sheets, double-layered boron sheets can form interlayer bonds, and the most stable one is semiconducting. Built from single-layered boron sheets, single-walled boron nanotubes have smaller curvature energies than carbon nanotubes and undergo a metal-to-semiconductor transition once the diameter is smaller than ˜20 A. Optimal double-walled boron nanotubes with inter-walled bonds formed are metallic and always more stable than single-walled ones. For Mg boride nanostructures, certain Mg boride sheets prefer to curve themselves into nanotubes, which is explained via Mg-Mg interactions governed by the charge state of Mg. In addition, optimal Mg boride sheet structures are explored with a genetic algorithm. Phase diagrams for Mg boride sheet structures are constructed and stable phases under boron-rich environments are identified. Curvature effects on the phase diagram of Mg boride nanotubes are also discussed. As a natural extension to boron sheets, layered boron crystals based on boron sheets are then presented and are shown to be stable under high pressure. Finally, this thesis ends with an investigation of hydrogen-storage properties of pristine and metal doped boron nanostructures.

This thesis conducts investigations mainly on the structures, energetics, and recations of semiconductor as well as oxide surfaces using firstprinciples cluster model approach. The first part of the research work addresses the issues in the epitaxial growth of Hgsb{1-x}Cdsb{x}Te (MCT) materials. Hg divalent compounds were studied thoroughly using a variety of quantum chemical methods in order to understand the energetics of Hg precursors for growth. The (001) growth surfaces were then examined in detail using cluster model calculations. Based on these results, a novel metal-organic molecular beam epitaxial (MOMBE) growth strategy with favorable energetics for growing MCT using Hsb2C=CH-CHsb2-Hg-Cequiv C-CHsb3 is proposed. It is hoped that with this new growth strategy, the Hg vacancy and p-doping problems that currently exist in growth can be avoided. The second part of the thesis discusses the molecular beam epitaxial (MBE) growth of cubic GaN on the (001) surface using various N sources. Surface reconstructions and the interactions of gas-phase atomic and molecular nitrogens with the surface were elucidated using cluster models. Using these results an energy phase diagram for the growth of GaN has been constructed. It suggests that excited state molecular Nsb2\\ (sp3Sigmasbsp{u}{+}) is the most favorable of all N species for growth of high quality GaN because it can undergo a dissociative chemisorption process. Ground state atomic N\\ (sp4S) is also good for growth. The doublet excited states N\\ (sp2D and sp2P) might cause surface N abstraction, leading to N vacancies in the material. Finally, a Fe(OH)sb3(Hsb2O)sb3 GVB cluster model of crystalline alpha-Fesb2Osb3 was developed. This simple model can describe the local geometry and bonding of Fe in the bulk oxide. Using quantum mechanical calculations, the orientation of the oleic imidazoline (OI) molecule bonding to the oxide surface has been determined. OI class of molecules are used extensively for corrosion inhibitor in oil field pipeline applications. It is found in this work that OI can make very strong bonding to the Fe of the iron oxide. In aqueous environments they can replace water on the pipe surface to form a protective layer to prevent corrosion.

We have studied the properties of spinel and layered cathode materials for Li ion rechargeable batteries. The analysis was done by firstprinciple calculations, and experimental techniques to elucidate materials that can substitute the presently commercialized material, namely LiCoO 2. We have studied the influence of Ni substitution for Mn in spinel Li 2MnO4. To understand the effects of this substitution on the crystal structure and electronic properties, firstprinciple DFT calculations were performed using VASP. The substitution was done systematically for up to 25% of Mn replacement by Ni in a super cell configuration. Furthermore, the influence of Ni substitution on lithium hoping pathways between the two stable Li positions was also studied by firstprinciple calculations in LiMn 2-xNixO4. These calculations revealed that Ni substitution for Mn in LiMn2O4 indeed improved Li ion mobility. Thereafter, systematic experimental studies were performed on LiMn 2-xNixO4 (0spectroscopy. The electrochemical performance of LiMn2-xNi xO4 materials was evaluated in two electrode CR2032 type coin cell configuration with Li metal as anode and liquid electrolyte (1 M LiPF6 in EC:DMC=1:1 v/v). Our results showed significant enhancement in the electrochemical properties with 25% of Ni substitution in LiMn 2O4, which is in good agreement with the theoretical calculations. We also studied layered cathode materials both theoretically and experimentally. The Firstprinciple calculations in conjunction with alloy metal method were used to evaluate the average voltage and phase stability of LiMO2 (M=Co, Ni, Mn, W) systems. By formation energy analysis we established that LiNi0.8Co0.1Mn0.1O2 is a promising candidate cathode material. Single-phase layered LiNi0.8Co 0.1Mn0.1O2 structure with hexagonal unit cell having R3¯m symmetry was synthesized by solid state route. The average particle size was around 6 mum. The electrochemical studies showed single redox reaction. Ex situ structural studies by XRD and Raman scattering at various stages of charging and discharging showed that the host layered structure is maintained throughout the electrochemical lithiation--delithiation processes in the 3--4.5V range with systematic change in the lattice parameters. First discharge capacity of LiNi0.8Co0.1Mn 0.1O2 was ˜132 mAh g-1 and the capacity retention was ˜86% after 20 charge--discharge cycles.

The structural and electronic properties of Rutherfordium, the newest group IV B element, have been evaluated by firstprinciples density functional theory in scalar relativistic formalism with and without spin-orbit coupling and compared with the known experimental and theoretical properties of its homologue Hf. It is found that it will crystallize in the hexagonal close packed structure with metallic character.

Photovoltaic cells based on SnS as the absorber layer show promise for efficient solar devices containing non-toxic materials that are abundant enough for large scale production. The efficiency of SnS cells has been increasing steadily, but various loss mechanisms in the device, related to the presence of defects in the material, have so far limited it far below its maximal theoretical value. In this work we perform firstprinciples, density-functional-theory calculations to examine the behavior and nature of both intrinsic and extrinsic defects in the SnS absorber layer. We focus on the elements known to exist in the environment of SnS-based photovoltaic devices during growth. In what concerns intrinsic defects, our calculations support the current understanding of the role of the Sn vacancy (VSn) acceptor defect, namely that it is responsible for the p-type conductivity in SnS. We also present calculations for extrinsic defects and make extensive comparison to experimental expectations. Our detailed treatment of electrostatic correction terms for charged defects provides theoretical predictions on both the high-frequency and low-frequency dielectric tensors of SnS. PMID:25363023

In the past decades, the steady increasing in both computer power and the efficiency of computational methods has made it realistic the accurate first-principles calculations of material properties at finite temperature. The current frontier is how to extend the first-principles approach when it becomes important of the role of the internal degrees of freedom, which is beyond the spatial degrees

First-principles study of multiferroic oxides Tamio OGUCHI Department of Quantum Matter, ADSM progress in the first-principles approach to multiferroic systems is reviewed. The elec- tronic structure and lattice stability of the known multiferroic BiMnO3 and the related oxides PbVO3 and BiCoO3

Spectroscopies resolved highly in momentum, energy and/or spatial dimensions are playing an important role in unraveling key properties of wide classes of novel materials. However, spectroscopies do not usually provide a direct map of the underlying electronic spectrum, but act as a complex 'filter' to produce a 'mapping' of the underlying energy levels, Fermi surfaces (FSs) and excitation spectra. The connection between the electronic spectrum and the measured spectra is described as a generalized 'matrix element effect'. The nature of the matrix element involved differs greatly between different spectroscopies. For example, in angle-resolved photoemission (ARPES) an incoming photon knocks out an electron from the sample and the energy and momentum of the photoemitted electron is measured. This is quite different from what happens in K-edge resonant inelastic X-ray scattering (RIXS), where an X-ray photon is scattered after inducing electronic transitions near the Fermi energy through an indirect second order process, or in Compton scattering where the incident X-ray photon is scattered inelastically from an electron transferring energy and momentum to the scattering electron. For any given spectroscopy, the matrix element is, in general, a complex function of the phase space of the experiment, e.g. energy/polarization of the incoming photon and the energy/momentum/spin of the photoemitted electron in the case of ARPES. The matrix element can enhance or suppress signals from specific states, or merge signals of groups of states, making a good understanding of the matrix element effects important for not only a robust interpretation of the spectra, but also for ascertaining optimal regions of the experimental phase space for zooming in on states of the greatest interest. In this thesis I discuss a comprehensive scheme for modeling various highly resolved spectroscopies of the cuprates and topological insulators (TIs) where effects of matrix element, crystal structure, strong electron correlations (for cuprates) and spin-orbit coupling (for TIs) are included realistically in material-specific detail. Turning to the cuprates, in order to obtain a realistic description of various spectroscopies, one must include not only the effects of the matrix elements and the complexity of the crystal structure, but also of strong electronic correlations beyond the local density approximation (LDA)-based conventional picture, so that the physics of kinks, pseudogaps and superconductivity can be taken into account properly. In this connection, a self-consistent, intermediate coupling scheme informed by material-specific, first-principles band structures has been developed, where electron correlation effects beyond the LDA are incorporated via appropriate self-energy corrections to the electron and hole one-particle Green's functions. Here the antiferromagnetic (AFM) order is used as the simplest model of a competing order. A number of salient features of the resulting electronic spectrum and its energy, momentum and doping dependencies are in accord with experimental observations in electron as well as hole doped cuprates. This scheme thus provides a reasonable basis for undertaking a comprehensive, beyond-LDA level of modeling of various spectroscopies. The specific topics considered here are: (i) Origin of high-energy kink or the waterfall effect found in ARPES; (ii) Identification of the three energy scales observed in RIXS spectra as the pseudogap, charge transfer gap, and Mott gap; (iii) Evolution of the electron momentum densities with holedoping as seen in Compton scattering experiments. For three dimensional topological insulators, the ARPES and scanning tunneling microscopy (STM) spectra has been analyzed using a tight-binding model as well as a k · p model. The spin-orbit coupling, which is essential to produce the characteristic features of the surface states of a TI, is included realistically in the above models. In our generalized k · p model Dresselhaus spin-orbit coupling term extends up to fifth order to reproduce the c

Recently, the vibrational signatures related to oxygen defects in oxygen-doped CdSe were measured using ultrahigh resolution Fourier transform infrared (FTIR) spectroscopy by Chen et al.(2008) [1]. They observed two absorption bands centered at ?1991.77 and 2001.3 cm-1, which they attributed to the LVMs of OCd, in the samples grown with the addition of CdO and excess Se. For the samples claimed to be grown with even more excess Se, three high-frequency modes (1094.11, 1107.45, and 1126.33) were observed and assigned to the LVMs of OSe-VCd complex. In this work, we explicitly calculated the vibrational signatures of OCd and OSe-VCd complex defects based on firstprinciples approach. The calculated vibrational frequencies of OCd and OSe-VCd complex are inconsistent with the frequencies observed by Chen et al., indicating that their observed frequencies are from other defects. Potential defects that could explain the experimentally observed modes are suggested.

We investigated structural changes, phase diagram, and vibrational properties of hydrogen hydrate in filled-ice phase C(2) by using firstprinciples molecular dynamics simulation. It was found that the experimentally reported "cubic" structure is unstable at low temperature and/or high pressure: The "cubic" structure reflects the symmetry at high (room) temperature where the hydrogen bond network is disordered and the hydrogen molecules are orientationally disordered due to thermal rotation. In this sense, the "cubic" symmetry would definitely be lowered at low temperature where the hydrogen bond network and the hydrogen molecules are expected to be ordered. At room temperature and below 30 GPa, it is the thermal effects that play an essential role in stabilizing the structure in "cubic" symmetry. Above 60 GPa, the hydrogen bonds in the framework would be symmetrized and the hydrogen bond order-disorder transition would disappear. These results also suggest the phase behavior of other filled-ice hydrates. In the case of rare gas hydrate, there would be no guest molecules' rotation-nonrotation transition since the guest molecules keep their spherical symmetry at any temperature. On the contrary methane hydrate MH-III would show complex transitions due to the lower symmetry of the guest molecule. These results would encourage further experimental studies, especially nuclear magnetic resonance spectroscopy and neutron scattering, on the phases of filled-ice hydrates at high pressures and/or low temperatures. PMID:22938248

We report the results of first-principles calculations (generalized gradient approximation-Perdew Wang 1991) on the electronic and vibrational properties of several nickel sulfides that are observed on Ni-based anodes in solid oxide fuel cells (SOFCs) upon exposure to H2S contaminated fuels: heazlewoodite Ni3S2, millerite NiS, polydymite Ni3S4, and pyrite NiS2. The optimized lattice parameters of these sulfides are within 1% of the values determined from x-ray diffraction. The electronic structure analysis indicates that all Ni-S bonds are strongly covalent. Furthermore, it is found that the nickel d orbitals shift downward in energy, whereas the sulfur p orbitals shift upward with increasing sulfur content; this is consistent with the decrease in conductivity and catalytic activity of sulfur-contaminated Ni-based electrodes (or degradation in SOFC performance). In addition, we systematically analyze the classifications of the vibrational modes at the point from the crystal symmetry and calculate the corresponding vibrational frequencies from the optimized lattice constants. This information is vital to the identification with in situ vibrational spectroscopy of the nickel sulfides formed on Ni-based electrodes under the conditions for SOFC operation. Finally, the effect of thermal expansion on frequency calculations for the Ni3S2 system is also briefly examined. PMID:18067373

Using a recently developed strong-coupling method, we present a comprehensive theory for doublon production processes in modulation spectroscopy of a three-dimensional system of ultracold fermionic atoms in an optical lattice with a trap. The theoretical predictions compare well to the experimental time traces of doublon production. For experimentally feasible conditions, we provide a quantitative prediction for the presence of a nonlinear "two-photon" excitation at strong modulation amplitudes.

By using developed particle swarm optimization algorithm on crystal structural prediction, we have explored the possible crystal structures of B-C system. Their structures, stability, elastic properties, electronic structure, and chemical bonding have been investigated by first-principles calculations with density functional theory. The results show that all the predicted structures are mechanically and dynamically stable. An analysis of calculated enthalpy with pressure indicates that increasing of boron content will increase the stability of boron carbides under low pressure. Moreover, the boron carbides with rich carbon content become more stable under high pressure. The negative formation energy of predicted B5C indicates its high stability. The density of states of B5C show that it is p-type semiconducting. The calculated theoretical Vickers hardnesses of B-C exceed 40 GPa except B4C, BC, and BC4, indicating they are potential superhard materials. An analysis of Debye temperature and electronic localization function provides further understanding chemical and physical properties of boron carbide.

Magnetic phase transitions that involve multipolar degrees of freedom have been widely studied during the last couple of decades, challenging the common approximation which assumes that the physical properties of a magnetic material could be effectively described by purely dipolar degrees of freedom. Due to the complexity of the problem and to the large number of competing interactions involved, the simple (fcc) crystal structure of the actinide dioxides made them the ideal playground system for such theoretical and experimental studies. In the present paper, we summarize our recent attempts to provide an ab initio description of the ordered phases of UO2, NpO2, and AmO2 by means of state-of-the-art LDA+U first-principles calculations. This systematic analysis of the electronic structures is here naturally connected to the local crystalline fields of the 5f states in the actinide dioxide series. Related to these we find that the mechanisms which lead to the experimentally observed insulating ground states work in distinctly different ways for each compound. xml:lang="fr"

We developed and implemented a first-principles based theory of the Landauer ballistic conductance, to determine the transport properties of nanostructures and molecular-electronics devices. Our approach starts from a ...

This thesis focuses on the design of novel inorganic water-splitting photocatalysts for solar applications using firstprinciples computations. Water-splitting photocatalysts are materials that can photo-catalyze the ...

This work is dedicated to development of a first-principle approach to study electron-vibration interactions on quantum transport properties. In the first part we discuss a general implementation for inelastic transport ...

Firstprinciples computation can be used to investigate an design materials in ways that can not be achieved with experimental means. We show how computations can be used to rapidly capture the essential physics that ...

Acephate is an insecticide that kills insects by disrupting nervous system functions. THz spectroscopy offers a unique tool for detecting trace amount of these materials. Using a combination of solid state firstprinciples simulations and gas phase quantum mechanical modeling we have studied phonon spectra of acephate compound. This talk will present a detailed vibrational spectra analysis over a wide range of frequency and our computational data will be compared with available experimental results.

The rich spectroscopy of the ethyl radical has attracted the attention of several experimental and theoretical investigations. The purpose of these studies was to elucidate the signatures of hyperconjugation, torsion, inversion, and Fermi coupling in the molecular spectra. Due to the number of degrees of freedom in the system, previous theoretical studies have implemented reduced-dimensional models. Our ultimate goal is a full-dimensional theoretical treatment of the vibrations using both Van Vleck and variational approaches. The methods will be combined with the potential that we have calculated using the CCSD(T) method on the cc-pVTZ basis set. In this talk we will discuss our initial work, which builds up from these reduced-dimensional models. Our calculations use coordinates that exploit the system's G_{12} PI symmetry in a simple fashion. By systematically adding more degrees of freedom to our model, we can determine the effects of specific couplings on the spectroscopy. T. Häber, A. C. Blair, D. J. Nesbitt and M. D. Schuder J. Chem. Phys. {124}, 054316, (2006). G .E. Douberly, unpublished. R. S. Bhatta, A. Gao and D. S. Perry J. Mol. Struct.: THEOCHEM {941}, 22, (2010).

Within the framework of the quasi-harmonic approximation, the thermodynamic properties and the phase transition of ThO2 from the cubic structure to the orthorhombic structure are studied using the first-principles projector-augmented wave method. The vibrational contribution to Helmholtz free energy is evaluated from the first-principles phonon density of states and the Debye-Grüneisen model. The calculated results reveal that at ambient temperature, the phase transition from the cubic phase to the orthorhombic phase occurs at 26.49 GPa, which is in agreement with the experimental and theoretical data. With increasing temperature, the transition pressure decreases almost linearly above room temperature. The predicted heat capacity and linear thermal expansion coefficient of cubic ThO2 are in good consistence with the experimental data. By comparing the experimental results with the calculation results from the first-principles and Debye-Grüneisen model, it is found that the thermodynamic properties of ThO2 are depicted well by the first-principles phonon treatment after including the an-harmonic correction to quasi-harmonic free energy.

Thermophysical properties, such as heat capacity, bulk modulus and thermal expansion, are of great importance for many technological applications and are traditionally determined experimentally. With the rapid development of computational methods, however, first-principles computed temperature-dependent data are nowadays accessible. We evaluate various computational realizations of such data in comparison to the experimental scatter. The work is focussed on the impact of different first-principles codes (QUANTUM ESPRESSO and VASP), pseudopotentials (ultrasoft and projector augmented wave) as well as phonon determination methods (linear response and direct force constant method) on these properties. Based on the analysis of data for two pure elements, Cr and Ni, consequences for the reliability of temperature-dependent first-principles data in computational thermodynamics are discussed. PMID:25071092

The understanding of metallic magnetism is of fundamental importance for a wide range of technological applications ranging from thin film disc drive read heads to bulk magnets used in motors and power generation. In this submission for the Gordon Bell Prize we use the power of massively parallel processing (MPP) computers to perform firstprinciples calculations of large system models

Silicon nanoclusters have significant interest due to their potential application to optoelectronic devices in visible range. Using firstprinciples approach, we investigate the electronic and optical properties of hydrogenated silicon nanoclusters. The highest occupied molecular orbital (HOMO) -- lowest unoccupied molecular orbital (LUMO) gap dependence on the cluster size show the same trend by using any exchange-correlation functionals. However, a

We propose a design strategy - based on the coupling of spins, optical phonons, and strain - for systems in which magnetic (electric) phase control can be achieved by an applied electric (magnetic) field. Using first-principles density-functional theory calculations, we present a realization of this strategy for the magnetic perovskite EuTiO3.

We propose a design strategy - based on the coupling of spins, optical phonons, and strain - for systems in which magnetic (electric) phase control can be achieved by an applied electric (magnetic) field. Using first-principles density-functional theory calculations, we present a realization of this strategy for the magnetic perovskite EuTiO3.

There are two main difficulties for the firstprinciples study of transport properties at the nano scale. The first is that many-body interactions need to be taken into account for the infinite system without periodic boundary conditions. The other is that the system is usually in a non-equilibrium state. Both of these two difficulties are beyond the ability of conventional

Materials that combine magnetic and ferroelectric properties have generated increasing interest over the last few years, due to both their diverse properties and their potential utility in new types of magnetoelectric device applications. In this review we discuss recent progress in the study of such magnetoelectric multiferroics which has been achieved using computational first-principles methods based on density functional theory.

Topological insulators are electronic materials that have a bulk band gap like an ordinary insulator but have protected conducting states on their edge or surface. The exotic electronic properties of topological materials are of great interest for spin-related electronics and quantum computation. In this thesis research, the combination of angleresolved photoemission spectroscopy (ARPES) and firstprinciples calculation is used to examine the electronic properties of topological thin films and 2D electronic systems with large spin-orbit splitting. The topological thin films are prepared in situ by molecular beam epitaxy (MBE) method and characterized by experimental tools such as reflection high-energy electron diffraction (RHEED) and low energy electron diffraction (LEED). The systems investigated in this thesis include topological Sb, Bi2Te3, Be2Se 3 thin films, Bi films, and Bi/Ag surface alloy. Topological Sb films have been successfully fabricated on Si(111) substrates. By examining the connection pattern between surface states and the quantum well bulk states, our photoemission spectra show clearly the topological order of the Sb films. When topological films become ultrathin, the quantum tunneling effect breaks the degeneracy at the Dirac point of the topological surface bands, resulting in a gap. Our ARPES mapping of the surface band structure of a 4-BL Sb film reveals no energy gap at the Dirac point. This lack of tunneling gap can be explained by a strong interfacial bonding between the film and the substrate. The topological order of topological materials is a robust quantity, but the topological surface states themselves can be highly sensitive to the boundary conditions. Specifically, the surface states of Bi2Se3 and Bi2Te3 form a single Dirac cone at the zone center. Our first-principles calculations based on a slab geometry show that, upon hydrogen termination of either face of the slab, the Dirac cone associated with this face is replaced by three Dirac cones centered at the time-reversal-invariant M¯ points at the zone boundary. The critical behavior of the TI film near the quantum critical point is also studied theoretically. When the strength of the spin-orbit coupling (SOC) is tuned across the critical point, the topological surface states, while protected by symmetry in the bulk limit, can be missing completely in topological films even at large film thicknesses. We have observed, using angle-resolved photoemission, a structural phase transformation of Bi films deposited on Si(111)-(7x7). Films with thicknesses 20 to ~100 A, upon annealing, first order into a metastable pseudocubic (PC) phase and then transform into a stable rhombohedral (RH) phase with very different topologies for the quantum well subband structures. The PC phase shows a surface band with a maximum near the Fermi level at G , whereas the RH phase shows a Dirac-like subband around M¯ along K¯ -- M¯ -- K¯ . The formation of the metastable phase over a wide thickness range can be attributed to a surface nucleation mechanism. Finally, we have studied the electronic structure of the Bi/Ag surface alloy, a system possessing a huge Rashba splitting in its surface bands. The Bi/Ag surface alloy is prepared by depositing Bi onto ultrathin Ag films followed by annealing. The electronic structure of the system is measured using circular angle resolved photoemission spectroscopy (CARPES). The results reveal two interesting phenomena: the hybridization of spin polarized surface states with Ag bulk quantum well states and the umklapp scattering by the perturbed surface potential. In addition, our CARPES spectra show clearly a unique dichroism pattern which is closely related to the spin texture of this 2D strongly spin-orbit coupled electron system.

Silicon is viewed as an excellent electrode material for lithium batteries due to its high lithium storage capacity. Various Si nanostructures, such as Si nanowires, have performed well as lithium battery anodes and have opened up exciting opportunities for the use of Si in energy storage devices. The mechanism of lithium insertion and the interaction between Li and the Si electrode must be understood at the atomic level; this understanding can be achieved by first-principles simulation. Here, first-principles computations of lithiation in silicon electrodes are reviewed. The review focuses on three aspects: the various properties of bulk Li-Si compounds with different Li concentrations, the electronic structure of Si nanowires and Li insertion behavior in Si nanowires, and the dynamic lithiation process at the Li/Si interface. Potential study directions in this research field and difficulties that the field still faces are discussed at the end.

Ferromagnet/graphene (F/Gr) junctions are important building blocks for graphene spintronics. While simple models of spin injection are very successful for macroscopic metallic junctions, they reveal many deficiencies in describing F/Gr junctions. First-principles methods are key to assess such Gr-based junctions, but the computational cost is often too high. We focus on Ni(111)/Gr junctions and include van der Waals interactions from firstprinciples, crucial for their correct description. We formulate a computationally inexpensive model to examine the nonuniformity and bias dependence of spin injection and elucidate proximity effects using spin polarization maps. Our results could extend the applicability of simple spin injection models in F/Gr junctions.

Completeness, efficiency and autonomy are requirements for suture diagnostic reasoning systems. Methods for automating diagnostic reasoning systems include diagnosis from firstprinciples (i.e., reasoning from a thorough description of structure and behavior) and diagnosis from experiential knowledge (i.e., reasoning from a set of examples obtained from experts). However, implementation of either as a single reasoning method fails to meet these requirements. The approach of combining reasoning from firstprinciples and reasoning from experiential knowledge does address the requirements discussed above and can possibly ease some of the difficulties associated with knowledge acquisition by allowing developers to systematically enumerate a portion of the knowledge necessary to build the diagnosis program. The ability to enumerate knowledge systematically facilitates defining the program's scope, completeness, and competence and assists in bounding, controlling, and guiding the knowledge acquisition process.

accepted version at constant temperature (T )i sR = i0M 0.75 , where i0 is a constant. We argue that, for zooplankton, a F-based, O2- consuming algorithm is more consistent with the cause of respiration. Our point: although biomass is related to respiration, the first- principles cause of respiration is ETS, because it controls O2 consumption. Biomass itself is indirectly

A comparative firstprinciples study has been carried out for EuLiH3 (ELH) and EuTiO3 (ETO) using the generalized gradient approximation +U approach. While ELH exhibits ferromagnetic ground state for all volumes, the magnetic ground state of ETO has the tendency to switch from G-type antiferromagnetic to a ferromagnetic state with change in volume. The marked difference in magnetic behavior and

Firstprinciples phonon dispersion relations are reported for a range of magnetic perovskite oxides in cubic high-symmetry reference structures. Materials considered include EuTiO3 and BiFeO3. For each system, the dominant lattice instabilities are identified. These are frozen-in, singly and in combination, and the structures are optimized in the resulting space groups. From this, we identify distinct low-energy alternatives to the

This is an exciting time for studying thiolated gold nanoclusters. Single crystal structures of Au{sub 102}(SR){sub 44} and Au{sub 25}(SR){sub 18}{sup -} (-SR being an organothiolate group) bring both surprises and excitement in this field. Firstprinciples density functional theory (DFT) simulations turn out to be an important tool to understand and predict thiolated gold nanoclusters. In this review, I summarize the progresses made by us and others in applying firstprinciples DFT to thiolated gold nanoclusters, as inspired by the recent experiments. First, I will give some experimental background on synthesis of thiolated gold nanoclusters, followed by a description of the recent experimental breakthroughs. Then I will introduce the superatom complex concept as a way to understand the electronic structure of thiolated gold nanoclusters or smaller nanoparticles. Next, I will describe in detail how firstprinciples DFT is used to understand the Au-thiolate interface, predict structures for Au{sub 38}(SR){sub 24}, screen good dopants for the Au{sub 25}(SR){sub 18}{sup -} cluster, design the smallest magic thiolated gold cluster, and demonstrate the need for the trimer protecting motif. I will conclude with a grand challenge: the real time monitoring of nucleation of thiolated gold nanoclusters.

Modeling the interface of Li metal and Li solid electrolytes from firstprinciples Nicholas Lepley battery electrolytes. Simplified theoretical models often fail to agree with experimental observations of the stability of electrode electrolyte interfaces. An example of this disagreement is the thiophosphate

We perform a first-principles study of the mechanical and vibrational properties of ZnS with a wurtzite structure. The calculated elastic constants by using a pseudopotential plane-wave method agree well with the experimental data and with the previous theoretical works. Based on the elastic constants and their related parameters, the crystal mechanical stability is discussed. Calculations of the zone-center optical-mode frequencies including longitudinal-optical/transverse-optical splitting, by using the density functional perturbation theory, are reported. All optical modes are identified, especially B1 modes, and agree with Raman measurements.

Recent advances in computational techniques have led to the possibility of performing firstprinciples calculations of the energetics of alloy formation on systems involving several hundred atoms. This includes impurity concentrations in the 1% range as well as realistic models of disordered materials (including liquids), vacancies, and grain boundaries. The new techniques involve the use of soft, fully nonlocal pseudopotentials, iterative diagonalization, and parallel computing algorithms. This approach has been pioneered by Car and Parrinello. Here the authors give a review of recent results using parallel and serial algorithms on metallic systems including liquid aluminum and liquid sodium, and also new results on vacancies in aluminum and on aluminum-magnesium alloys.

In this paper, thermal conductivity of crystalline GaAs is calculated using first-principles lattice dynamics. The harmonic and cubic force constants are obtained by fitting them to the force-displacement data from density functional theory calculations. Phonon dispersion is calculated from dynamical matrix constructed using the harmonic force constants and phonon relaxation times are calculated using Fermi's Golden rule. The calculated GaAs thermal conductivity agrees well with experimental data. Thermal conductivity accumulations as a function of phonon mean free path and as a function of wavelength are obtained. Our results predict significant size effect on the GaAs thermal conductivity in the nanoscale.

The methylammonium lead iodide perovskites at the core of recently proposed solar cells with exceptionally large quantum conversion efficiency are studied by first-principles methods. Large absorption coefficients (0.03-0.04 nm-1 for wavelength ˜500 nm) and small effective masses suited for both n-type and p-type transport are obtained as a consequence of their peculiar structural and electronic characteristics. In particular, the presence of a direct gap between highly dispersed Pb(6s)-I(5p) valence bands and Pb(6p) conduction bands is the key ingredient at the basis of their excellent performance in photovoltaic applications.

We provide a detailed derivation of a recently developed first-principles approach to calculating averages in systems of interacting, spherical Brownian particles under time-dependent flow. Although we restrict ourselves to flows which are both homogeneous and incompressible, the time-dependence and geometry (e.g. shear, extension) are arbitrary. The approximations formulated within mode-coupling theory are particularly suited to dense colloidal suspensions and capture the slow relaxation arising from particle interactions and the resulting glass transition to an amorphous solid. The delicate interplay between slow structural relaxation and time-dependent external flow in colloidal suspensions may thus be studied within a fully tensorial theory.

We report a combined experimental and theoretical study of the unoccupied electronic states of the neutral molecular organic materials TTF (tetrathiafulvalene) and TCNQ (7,7,8,8-tetracyano-p-quinodimethane) and of the one-dimensional metallic charge transfer salt TTF-TCNQ. The experimental density of states (DOS) is obtained by x-ray absorption near edge spectroscopy (XANES) with synchrotron light and the predicted DOS by means of first-principles density functional theory calculations. Most of the experimentally derived element-specific XANES features can be associated to molecular orbitals of defined symmetry. Because of the planar geometry of the TTF and TCNQ molecules and the polarization of the synchrotron light, the energy dependent ? or ? character of the orbitals can be inferred from angular dependent XANES measurements. The present work represents the state of the art analysis of the XANES spectra of this type of materials and points out the need for additional work in order to elucidate the governing selection rules in the excitation process.

In the past decades, the steady increasing in both computer power and the efficiency of computational methods has made it realistic the accurate first-principles calculations of material properties at finite temperature. The current frontier is how to extend the first-principles approach when it becomes important of the role of the internal degrees of freedom, which is beyond the spatial degrees of freedom of a material. One of important examples is the interplay between magnetic and lattice fluctuations at finite temperature. Solution of this enigma can reveal the microscopic origin of the novel properties of many materials. Hereby we propose a general framework to calculate the Helmholtz energy for system with spin fluctuations. The theory has been applied for EuTiO3. The energetics includes 256 spin configurations, of a 2x2x2 supercell, which are reduced to 14 not equivalent ones. We find a Schottky anomaly in the specific heat at T = 5.8 K which is matching closely to the Neel Temperature of 5.5 K for EuTiO3.

We have investigated inter-molecular interactions in weakly bonded molecular assemblies from firstprinciples, by combining exact exchange energies (EXX) with correlation energies defined by the adiabatic connection fluctuation-dissipation theorem, within the random phase approximation (RPA)[1,2]. We present results for three different types of molecular systems: the benzene crystal, the methane crystal and self-assembled monolayers of phenylenediisocyanide. We describe in detail how computed equilibrium lattice constants and cohesive energies may be affected by input ground state wave functions and orbital energies, by the geometries of the molecular monomers in the assemblies, and by the inclusion of zero point energy contribution to the total energy. We find that the EXX/RPA perturbative approach provides an overall satisfactory, firstprinciple description of dispersion forces, in good agreement with experiments and advanced quantum chemistry results. However, binding energies tend to be underestimated and possible reasons for this discrepancy are discussed. This work was funded by DOE/BES DE-FG02-06ER46262 and DOE/SciDAC DE-FC02-06ER25794.[1] Y. Li, D. Lu, H-V. Nguyen and G. Galli, J. Phys. Chem.(submitted). [2]D. Lu, Y. Li, D. Rocca and G. Galli, Phys. Rev. Lett. 102, 206411(2009).

Firstprinciples calculations are performed for the interpretation of the L?,? x-ray absorption spectrum of calcium oxide and calcium fluoride. The firstprinciples calculations are based on configuration interaction (CI) calculations using fully relativistic molecular spinors. The firstprinciples results are compared to experimental data and also to calculations based on a semi-empirical crystal field multiplet model and also on a multichannel multiple scattering method. We show that the CI calculations show good agreement with experiment, both for bulk and for surface experiments. The remaining differences with experiment and between the theoretical models are discussed in detail. PMID:21427477

There are two main difficulties for the firstprinciples study of transport properties at the nano scale. The first is that many-body interactions need to be taken into account for the infinite system without periodic boundary conditions. The other is that the system is usually in a non-equilibrium state. Both of these two difficulties are beyond the ability of conventional firstprinciples methods to reconcile. Recently, a new firstprinciples approach which combines the Non-equilibrium Green's Functions Technique (NGFT) and the Density Functional Theory (DFT) was proposed. DFT has been proved to be successful in molecular and solid state physics. Currently used DFT approximations can take into account 'most' many-body effects and NGFT naturally includes the non-equilibrium effects. The new approach uses NGFT to treat the non-periodic boundary conditions and DFT to treat many body interactions. This approach has been successfully used in molecular electronics. The thesis is organized in the following way. First: we introduce the main ideas of combining NGFT and DFT, and then apply this method to a light-driven molecular switch. The switch, made of a single molecule, is one of the most important elements of nano-electronics. However, most proposed molecular switches are driven either by an external bias voltage or by STM manipulation, neither of which is ideal for nano-scale circuits. The switch we designed has a high on-off conductance ratio and more importantly, can be driven by photons. In following chapters, we generalize the method to the spin-dependent case and apply it to a magnetic layered structure. We implemented the method within the framework of the Layer Korringa-Kohn-Rostoker (LKKR) approach, which is particularly well-adapted to the layered structure and found a bias-enhanced tunneling magneto-resistance (TMR) for the Fe/FeO/MgO/Fe junction. Our results are important not only for application, but also for understanding of the voltage-dependence of TMR for layered structures. The experimental studies show that the bias voltage usually kills the TMR of amorphous magnetic tunneling junctions. Our study shows that for an impurity-free layered structure, a different behavior of TMR may occur.

Quantum Chromodynamics (QCD) is generally assumed to be the fundamental theory underlying nuclear physics. In recent years there is progress towards investigating the nucleon structure from firstprinciples of QCD. Although this structure is best revealed in Deep Inelastic Scattering, a consistent analysis has to be performed in a fully non-perturbative scheme. The only known method for this purpose are lattice simulations. We first sketch the ideas of Monte Carlo simulations in lattice gauge theory. Then we comment in particular on the issues of chiral symmetry and operator mixing. Finally we present our results for the Bjorken variable of a single quark, and for the second Nachtmann moment of the nucleon structure functions.

Quantum Chromodynamics (QCD) is generally assumed to be the fundamental theory underlying nuclear physics. In recent years there is progress towards investigating the nucleon structure from firstprinciples of QCD. Although this structure is best revealed in Deep Inelastic Scattering, a consistent analysis has to be performed in a fully non-perturbative scheme. The only known method for this purpose are lattice simulations. We first sketch the ideas of Monte Carlo simulations in lattice gauge theory. Then we comment in particular on the issues of chiral symmetry and operator mixing. Finally we present our results for the Bjorken variable of a single quark, and for the second Nachtmann moment of the nucleon structure functions.

We present first-principles, density-functional theory calculations of the NMR chemical shifts for polycyclic aromatic hydrocarbons, starting with benzene and increasing sizes up to the one- and two-dimensional infinite limits of graphene ribbons and sheets. Our calculations are performed using a combination of the recently developed theory of orbital magnetization in solids, and a novel approach to NMR calculations where chemical shifts are obtained from the derivative of the orbital magnetization with respect to a microscopic, localized magnetic dipole. Using these methods we study on equal footing the 1H and 13C shifts in benzene, pyrene, coronene, in naphthalene, anthracene, naphthacene, and pentacene, and finally in graphene, graphite, and an infinite graphene ribbon. Our results show very good agreement with experiments and allow us to characterize the trends for the chemical shifts as a function of system size.

There has been much interest in the thin-film solid electrolyte for solid state battery and ionics applications. LiPON is a representative material developed by Oak Ridge National Laboratory [1]. In this work, we use firstprinciples calculations based on the density functional theory to investigate the Li- ion migration mechanisms of LiPON family materials [2]. We investigate atomic structures, electronic structures and defect formation energies of these materials. To determine the migration path of Li diffusion, the activation energies are calculated. This study helps us to understand fundamental mechanisms of Li-ion migration and to improve Li ion conductivity in the solid electrolytes. [4pt] [1] Patil et al, Material Research Bulletin, 43 (2008) 1913-1942. [0pt] [2] Yaojun A. Du and N. A. W. Holzwarth, Physical Review B, 81 (2010).

Structural and dynamical properties of the hydration of Li(+), Na(+), and K(+) in liquid water at ambient conditions were studied by firstprinciples molecular dynamics. Our simulations successfully captured the different hydration behavior shown by the three alkali ions as observed in experiments. The present analyses of the dependence of the self-diffusion coefficient and rotational correlation time of water on the ion concentration suggest that Li(+) (K(+)) is certainly categorized as a structure maker (breaker), whereas Na(+) acts as a weak structure breaker. An analysis of the relevant electronic structures, based on maximally localized Wannier functions, revealed that the dipole moment of H(2)O molecules in the first solvation shell of Na(+) and K(+) decreases by about 0.1 D compared to that in the bulk, due to a contraction of the oxygen lone pair orbital pointing toward the metal ion. PMID:17249878

Structural and dynamical properties of the hydration of Li+, Na+, and K+ in liquid water at ambient conditions were studied by firstprinciples molecular dynamics. Our simulations successfully captured the different hydration behavior shown by the three alkali ions as observed in experiments. The present analyses of the dependence of the self-diffusion coefficient and rotational correlation time of water on the ion concentration suggest that Li+ (K+) is certainly categorized as a structure maker (breaker), whereas Na+ acts as a weak structure breaker. An analysis of the relevant electronic structures, based on maximally localized Wannier functions, revealed that the dipole moment of H2O molecules in the first solvation shell of Na+ and K+ decreases by about 0.1 D compared to that in the bulk, due to a contraction of the oxygen lone pair orbital pointing toward the metal ion.

Olivine phosphates LiMPO4 (M=Mn, Fe, Co, Ni) are promising candidates for rechargeable Li-ion battery electrodes because of their energy storage capacity and electrochemical and thermal stability. It is known that native defects have strong effects on the performance of olivine phosphates. Yet, the formation and migration of these defects are not fully understood, and we expect that once such understanding has been established, one can envisage a solution for improving the materials' performance. In this talk, we present our first-principles density-functional theory studies of native point defects and defect complexes in LiMPO4, and discuss the implications of these defects on the performance of the materials. Our results also provide guidelines for obtaining different native defects in experiments.

Silicon nanoclusters have significant interest due to their potential application to optoelectronic devices in visible range. Using firstprinciples approach, we investigate the electronic and optical properties of hydrogenated silicon nanoclusters. The highest occupied molecular orbital (HOMO) -- lowest unoccupied molecular orbital (LUMO) gap dependence on the cluster size show the same trend by using any exchange-correlation functionals. However, a reasonable agreement to experimental absorption spectra peak values cannot be achieved from conventional LDA or GGA functional-based calculations. Using B3LYP hybrid functional within time-dependent density functional theory, we obtain excitonic energies in quantitatively good agreement to experimental data. The passivant effect on HOMO-LUMO gap and excitonic energies will be also presented.

We present a generalized approach for computing electron conductance and I-V characteristics in multiterminal junctions from first-principles. Within the framework of Keldysh theory, electron transmission is evaluated employing an O(N) method for electronic-structure calculations. The nonequilibrium Green function for the nonequilibrium electron density of the multiterminal junction is computed self-consistently by solving Poisson equation after applying a realistic bias. We illustrate the suitability of the method on two examples of four-terminal systems, a radialene molecule connected to carbon chains and two crossed-carbon chains brought together closer and closer. We describe charge density, potential profile, and transmission of electrons between any two terminals. Finally, we discuss the applicability of this technique to study complex electronic devices. PMID:19894925

We investigate the structural and magnetic properties of interfaces with large lattice mismatch, choosing Pt/Co and Au/Co as prototypes. For our first-principles calculations, we reduce the lattice mismatch to 0.2% by constructing Moiré supercells. Our results show that the roughness and atomic density, and thus the magnetic properties, depend strongly on the substrate and thickness of the Co slab. An increasing thickness leads to the formation of a Co transition layer at the interface, especially for Pt/Co due to strong Pt-Co interaction. A Moiré supercell with a transition layer is found to reproduce the main experimental findings and thus turns out to be the appropriate model for simulating magnetic misfit interfaces.

Phase stabilities and mechanical properties of ideal stoichiometric technetium monocarbide (TcC) and technetium mononitride (TcN) in the tungsten carbide (WC), nickel arsenide (NiAs), rocksalt (NaCl), and zinc-blende (ZnS) structures, respectively, have been studied systematically by first-principles calculations. It is found that both TcC and TcN in two hexagonal phases (WC and NiAs) are not only elastically stable but also hard and ultrastiff materials. Remarkably, for the two hexagonal TcC phases, both bulk moduli and linear incompressibilities along the c axis exceed that of c BN and even rival with diamond. Their hardness can also match the known hard materials such as WC. The combination of good metallicity, strong stiffness, and high hardness suggests that the materials may find applications as hard conductors and cutting tools.

We present a first-principles study of model domain walls (DWs) in prototypic ferroelectric PbTiO(3). At high temperature the DW structure is somewhat trivial, with atoms occupying high-symmetry positions. However, upon cooling the DW undergoes a symmetry-breaking transition characterized by a giant dielectric anomaly and the onset of a large and switchable polarization. Our results thus corroborate previous arguments for the occurrence of ferroic orders at structural DWs, providing a detailed atomistic picture of a temperature-driven DW-confined transformation. Beyond its relevance to the field of ferroelectrics, our results highlight the interest of these DWs in the broader areas of low-dimensional physics and phase transitions in strongly fluctuating systems. PMID:24996110

A comparative firstprinciples study has been carried out for EuLiH3 (ELH) and EuTiO3 (ETO) using the generalized gradient approximation +U approach. While ELH exhibits ferromagnetic ground state for all volumes, the magnetic ground state of ETO has the tendency to switch from G-type antiferromagnetic to a ferromagnetic state with change in volume. The marked difference in magnetic behavior and magnitude of the nearest neighbors exchange interaction of both the compounds are shown to be related to the difference in their respective electronic structure near the Fermi level. The Ti 3d states are shown to play predominant role in weakening the strength of the exchange interaction in ETO.

Phosphorene, the single layer counterpart of black phosphorus, is a novel two-dimensional semiconductor with high carrier mobility and a large fundamental direct band gap, which has attracted tremendous interest recently. Its potential applications in nano-electronics and thermoelectrics call for fundamental study of the phonon transport. Here, we calculate the intrinsic lattice thermal conductivity of phosphorene by solving the phonon Boltzmann transport equation (BTE) based on first-principles calculations. The thermal conductivity of phosphorene at $300\\,\\mathrm{K}$ is $30.15\\,\\mathrm{Wm^{-1}K^{-1}}$ (zigzag) and $13.65\\,\\mathrm{Wm^{-1}K^{-1}}$ (armchair), showing an obvious anisotropy along different directions. The calculated thermal conductivity fits perfectly to the inverse relation with temperature when the temperature is higher than Debye temperature ($\\Theta_D = 278.66\\,\\mathrm{K}$). In comparison to graphene, the minor contribution around $5\\%$ of the ZA mode is responsible for the low thermal cond...

We investigate the Dirac cone in ?-graphdiyne, which is a predicted flat one-atom-thick allotrope of carbon using first-principles calculations. ?-graphdiyne is derived from graphene where two acetylenic linkages (-C ?C-) are inserted into the single bonds (-C-C-). Thus, ?-graphdiyne possesses a larger lattice constant which subsequently affects its electronic properties. Band structures show that ?-graphdiyne exhibits similar Dirac points and cone to graphene. Further, the tight-binding method is used to exploit the linear dispersion in the vicinity of Dirac points. Thanks to the larger lattice constant, ?-graphdiyne yields a lower Fermi velocity, which might make itself an ideal material to serve the anomalous integer quantum Hall effect. PMID:24206912

We investigate the Dirac cone in ?-graphdiyne, which is a predicted flat one-atom-thick allotrope of carbon using first-principles calculations. ?-graphdiyne is derived from graphene where two acetylenic linkages (-C ?C-) are inserted into the single bonds (-C-C-). Thus, ?-graphdiyne possesses a larger lattice constant which subsequently affects its electronic properties. Band structures show that ?-graphdiyne exhibits similar Dirac points and cone to graphene. Further, the tight-binding method is used to exploit the linear dispersion in the vicinity of Dirac points. Thanks to the larger lattice constant, ?-graphdiyne yields a lower Fermi velocity, which might make itself an ideal material to serve the anomalous integer quantum Hall effect.

We present a first-principles study of model domain walls (DWs) in prototypic ferroelectric PbTiO3. At high temperature the DW structure is somewhat trivial, with atoms occupying high-symmetry positions. However, upon cooling the DW undergoes a symmetry-breaking transition characterized by a giant dielectric anomaly and the onset of a large and switchable polarization. Our results thus corroborate previous arguments for the occurrence of ferroic orders at structural DWs, providing a detailed atomistic picture of a temperature-driven DW-confined transformation. Beyond its relevance to the field of ferroelectrics, our results highlight the interest of these DWs in the broader areas of low-dimensional physics and phase transitions in strongly fluctuating systems.

Based on the nonequilibrium Green's function (NEGF) and time-dependent density-functional theory (TDDFT), we propose a formalism to study the time-dependent transport behavior of molecular devices from firstprinciples. While this approach is equivalent to the time-dependent wave-function approach within TDDFT, it has the advantage that the scattering states and bound states are treated on equal footing. Furthermore, it is much easier to implement our approach numerically. Different from the time-dependent wave-function [?(t,E)] approach, our formalism is in the time space [Gr(t,t')], making this method superior in the time-dependent transport problem with many subbands in the transverse direction. For the purpose of numerical implementation on molecular devices, a computational tractable numerical scheme is discussed in detail. We have applied our formalism to calculate the transient current of two molecular devices Al-1,4-dimethylbenzene-Al and Al-benzene-Al from firstprinciples. In the calculation, we have gone beyond the wideband limit and used the adiabatic local density approximation that was used within TDDFT. It is known that when the wideband limit is abandoned, the boundary condition of the transport problem is non-Markovian, resulting in a memory term in the effective Hamiltonian of the scattering region. To overcome the computational complexity due to the memory term, we have employed a fast algorithm to speed up the calculation and reduced the CPU time from the scaling N3 to N2log22(N) for the steplike pulse, where N is the number of time steps in the time evolution of the Green's function. To ensure the accuracy of our method, we have done a benchmark transient calculation on an atomic junction using a time-dependent wave-function approach within TDDFT in momentum space, which agrees very well with the result from our method.

Integration has traditionally been so closely linked to the interpretation as an area and to the techniques of anti-differentiation as to appear inseparable from them. While largely a consequence of the fact that, in pre-Personal-Computer times, anti-differentiation was the key to effective integration and that line and surface integrals were generally intractable using that technique, the advent of computer algebra systems and easy large scale numerical computation seems not to have had much effect on the way integration is presented in standard texts. On the one hand, it is not clear what sorts of skills are required for a novice to handle computer algebra effectively and on the other hand most available software does not provide the data structures and tools for dealing conveniently with numerical integration from firstprinciples in the general case. We focus on the latter. In this article we examine an approach to the principles of integration based on computer manipulation of multi-dimensional arrays for the coordinate grids, referring to the area interpretation as only one among several possibilities and presenting integration as the solution to non-trivial anti-differentiation problems. Underlying the implementation of the approach is the mathematical notation of Iversons J, an array-processing, functional, computer language. We suggest that the mathematical foundations of the topic existence of, and convergence to, the limit should be postponed till after students can effectively compute and manipulate the approximations that are used to define integrals from firstprinciples. Target Audience: 2-4 Year College Faculty/Administrators, Engineers

The nonresonant vibrational Raman spectra of tetrahedral amorphous carbon are calculated from firstprinciples. The structural model was generated using Car-Parinello molecular dynamics, the vibrational modes are determined using the linear response approach and Raman tensors are calculated using the finite electric field method. Our theoretical visible and reduced Raman spectra show an overall good agreement with experimental spectra, and better than previous calculated results. The analysis in terms of atomic vibrations shows that the Raman spectrum mainly comes from sp 2 contribution, G peak is due to the stretching vibration of any pair of sp 2 atoms and only a small sp 3 contribution can be noticed. The differences between peak intensities of reduced theoretical and experimental results mainly come from defects and the high sp 3 content in our simulated structure.

Some aspects of the functional RG (FRG) approach to pinned elastic manifolds (of internal dimension d) at finite temperature T > 0 are reviewed and reexamined in this much expanded version of Le Doussal (2006) . The particle limit d = 0 provides a test for the theory: there the FRG is equivalent to the decaying Burgers equation, with viscosity {nu} {approx} T-both being formally irrelevant. An outstanding question in FRG, i.e. how temperature regularizes the otherwise singular flow of T = 0 FRG, maps to the viscous layer regularization of inertial range Burgers turbulence (i.e. to the construction of the inviscid limit). Analogy between Kolmogorov scaling and FRG cumulant scaling is discussed. First, multi-loop FRG corrections are examined and the direct loop expansion at T > 0 is shown to fail already in d = 0, a hierarchy of ERG equations being then required (introduced in Balents and Le Doussal (2005) ). Next we prove that the FRG function R(u) and higher cumulants defined from the field theory can be obtained for any d from moments of a renormalized potential defined in an sliding harmonic well. This allows to measure the fixed point function R(u) in numerics and experiments. In d = 0 the beta function (of the inviscid limit) is obtained from firstprinciples to four loop. For Sinai model (uncorrelated Burgers initial velocities) the ERG hierarchy can be solved and the exact function R(u) is obtained. Connections to exact solutions for the statistics of shocks in Burgers and to ballistic aggregation are detailed. A relation is established between the size distribution of shocks and the one for droplets. A droplet solution to the ERG functional hierarchy is found for any d, and the form of R(u) in the thermal boundary layer is related to droplet probabilities. These being known for the d = 0 Sinai model the function R(u) is obtained there at any T. Consistency of the {epsilon}=4-d expansion in one and two loop FRG is studied from firstprinciples, and connected to shock and droplet relations which could be tested in numerics.

Doping graphene with electron donating or accepting molecules is an interesting approach to introduce carriers into it, analogous to electrochemical doping accomplished in graphene when used in a field-effect transistor. Here, we use first-principles density-functional theory to determine changes in the electronic-structure and vibrational properties of graphene that arise from the adsorption of aromatic molecules such as aniline and nitrobenzene. Identifying the roles of various mechanisms of chemical interaction between graphene and a molecule, we bring out the contrast between electrochemical and molecular doping of graphene. Our estimates of various contributions to shifts in the Raman-active modes of graphene with molecular doping are fundamental to the possible use of Raman spectroscopy in (a) characterization of the nature and concentration of carriers in graphene with molecular doping, and (b) graphene-based chemical sensors.

There is currently much interest in photoelectrochemical water splitting as a promising pathway towards sustainable energy production. A major issue of such photoelectrochemical devices is the limited efficiency of the anode, where the oxygen evolution reaction (OER) takes place. Cobalt (hydro)oxides, particularly Co3O4 and Co(OH)2, have emerged as promising candidates for use as OER anode materials. Interestingly, recent in-situ Raman spectroscopy studies have shown that Co3O4 electrodes undergo progressive oxidation and transform into oxyhydroxide, CoO(OH), under electrochemical working conditions. (Journal of the American Chemical Society 133, 5587 (2011))Using firstprinciple electronic structure calculations, we provide insight into these findings by presenting results on the structural, thermodynamic, and electronic properties of cobalt oxide, hydroxide and oxydroxide CoO(OH), and on their relative stabilities when in contact with water under external voltage.

Recently there has been much interest in development of new electrochemical capacitors to meet high-power and high-energy applications. Pseudo-capacitors using fast surface redox reactions can store electrical energy of 10 to 100 times larger than supercapacitors and still exhibit fast and reversible charge-discharge responses in contrast to batteries. Yet, energy storage mechanisms in super- and pseudo-capacitors have not been fully understood at the level of electrons. Here we have performed first-principles calculations for electrical double layers of a TiO2 (101) electrode and solvated lithium ions on the surface, with the ethylene carbonates (EC) as solvent molecules. As Li ions are desolvated from Li-EC4 to Li-EC3 and bare Li ions, the capacitance gets larger due to the reduced distance between the Li ions and the electrode. When Li ions are intercalated into the subsurface of the TiO2 electrode as supposed in pseudocapacitors, the electrostatic energy due to charge separation is reduced for a given stored charge, but the electrochemical reaction starts to occur causing a large increase in the capacitance.

Solid state ammonia borane (AB, H3BNH3) has attracted considerable attention as a promising hydrogen storage material. In this paper, electronic structures, bonding characters and hydrogen release mechanism of AB are investigated by first-principles calculations. From electronic structure calculations, we show that B (or N) atom first constructs sp hybrids and then forms covalent bonds with surrounding H atoms. The B-N bonds are formed via B-p and N-p hybridization and are dative in nature. Electron deficiency of B atoms induces a charge transfer, which results in hydrogen bonds and dipole-dipole interactions among H3BNH3 complexes. The hydrogen-bonding energy in AB is estimated to be 15.1 kJ mol-1. The formation enthalpy calculations indicate that, in the initial stage of the hydrogen release process, the H atoms forming an H2 molecule are decomposed from two adjacent H3BNH3 complexes rather than from the same H3BNH3 complex and the process is almost thermoneutral.

The ground-state electronic structures of the actinide oxides AO , A{sub 2} O{sub 3} , and AO{sub 2} (A=U , Np, Pu, Am, Cm, Bk, and Cf) are determined from first-principles calculations, using the self-interaction corrected local spin-density approximation. Emphasis is put on the degree of f -electron localization, which for AO{sub 2} and A{sub 2} O{sub 3} is found to follow the stoichiometry, namely, corresponding to A{sup 4+} ions in the dioxide and A{sup 3+} ions in the sesquioxides. In contrast, the A{sup 2+} ionic configuration is not favorable in the monoxides, which therefore become metallic. The energetics of the oxidation and reduction in the actinide dioxides is discussed, and it is found that the dioxide is the most stable oxide for the actinides from Np onward. Our study reveals a strong link between preferred oxidation number and degree of localization which is confirmed by comparing to the ground-state configurations of the corresponding lanthanide oxides. The ionic nature of the actinide oxides emerges from the fact that only those compounds will form where the calculated ground-state valency agrees with the nominal valency expected from a simple charge counting.

A new icing model has been developed to predict the sponginess (liquid fraction) and growth rate of freshwater ice accretions growing under a surface film of unfrozen water. This model is developed from firstprinciples and does not require experimental sponginess data to tune the model parameters. The model identifies icing conditions that include no accretion, dry accretion, glaze accretion, spongy nonshedding, and spongy shedding regimes. It is a steady state model for a stationary vertical cylinder intercepting horizontally directed spray. The model predicts both the accretion mass growth flux and the accretion sponginess. The model results suggest that spongy shedding and spongy nonshedding regimes are common under the high liquid flux conditions typical of freshwater ship icing. Moreover, the unfrozen liquid incorporated into the spongy ice matrix can substantially increase the ice accretion load over that which would be predicted purely thermodynamically. Despite differences in the experimental setup, the model's performance compares well with two independent freshwater experimental data sets for icing on horizontal rotating cylinders. The model performs well in its prediction of both accretion sponginess and growth rate. The model predicts sponginess with a variation in liquid mass fraction of about 0.2-0.5, over the range of air temperature of 0°C to -30°C, in agreement with observations.

GaN/ZnO alloy semiconductors have been shown to be promising materials to serve as photo-anode in photocatalytical fuel cells. In recent study by Shen et alootnotetextX. Shen, Y.A. Small, J. Wang, P.B. Allen, M.V. Fernandez-Serra, M.S. Hybertsen and J.T. Muckerman J. Phys. Chem. C 114(32), 13695 (2010), the non polar GaN(1010) surface has been studied with atomistic modeling and a sequence of intermediate steps for the water oxidation process at the interface are proposed. Here we present a firstprinciples molecular dynamics study of the GaN(1010)/Water interface. We found dissociation events happen within 1ps and we show a detailed analysis of the changes in structure and dynamics of water molecules interacting with a dissociating wet surface. The complex hydrogen bond network near the surface is also analyzed in detail, including a throughout study of the proton diffusion processes. We perform a detailed analysis of the dynamics of the hole localization. The link between water surface dissociation and quantum efficiency will be discussed.

The ground-state electronic structures of the actinide oxides AO, A{sub 2}O{sub 3}, and AO{sub 2} (A=U, Np, Pu, Am, Cm, Bk, and Cf) are determined from first-principles calculations, using the self-interaction corrected local spin-density approximation. Emphasis is put on the degree of f-electron localization, which for AO{sub 2} and A{sub 2}O{sub 3} is found to follow the stoichiometry, namely, corresponding to A{sup 4+} ions in the dioxide and A{sup 3+} ions in the sesquioxides. In contrast, the A{sup 2+} ionic configuration is not favorable in the monoxides, which therefore become metallic. The energetics of the oxidation and reduction in the actinide dioxides is discussed, and it is found that the dioxide is the most stable oxide for the actinides from Np onward. Our study reveals a strong link between preferred oxidation number and degree of localization which is confirmed by comparing to the ground-state configurations of the corresponding lanthanide oxides. The ionic nature of the actinide oxides emerges from the fact that only those compounds will form where the calculated ground-state valency agrees with the nominal valency expected from a simple charge counting.

The electrical conductance of atomic metal contacts represents a powerful tool for detecting nanomagnetism. Conductance reflects magnetism through anomalies at zero bias-generally with Fano line shapes-owing to the Kondo screening of the magnetic impurity bridging the contact. A full atomic-level understanding of this nutshell many-body system is of the greatest importance, especially in view of our increasing need to control nanocurrents by means of magnetism. Disappointingly, at present, zero-bias conductance anomalies are not calculable from atomistic scratch. Here, we demonstrate a working route connecting approximately but quantitatively density functional theory (DFT) and numerical renormalization group (NRG) approaches and leading to a first-principles conductance calculation for a nanocontact, exemplified by a Ni impurity in a Au nanowire. A Fano-like conductance line shape is obtained microscopically, and shown to be controlled by the impurity s-level position. We also find a relationship between conductance anomaly and geometry, and uncover the possibility of opposite antiferromagnetic and ferromagnetic Kondo screening-the latter exhibiting a totally different and unexplored zero-bias anomaly. The present matching method between DFT and NRG should permit the quantitative understanding and exploration of this larger variety of Kondo phenomena at more general magnetic nanocontacts.

The electrical conductance of atomic metal contacts represents a powerful tool for detecting nanomagnetism. Conductance reflects magnetism through anomalies at zero bias--generally with Fano line shapes--owing to the Kondo screening of the magnetic impurity bridging the contact. A full atomic-level understanding of this nutshell many-body system is of the greatest importance, especially in view of our increasing need to control nanocurrents by means of magnetism. Disappointingly, at present, zero-bias conductance anomalies are not calculable from atomistic scratch. Here, we demonstrate a working route connecting approximately but quantitatively density functional theory (DFT) and numerical renormalization group (NRG) approaches and leading to a first-principles conductance calculation for a nanocontact, exemplified by a Ni impurity in a Au nanowire. A Fano-like conductance line shape is obtained microscopically, and shown to be controlled by the impurity s-level position. We also find a relationship between conductance anomaly and geometry, and uncover the possibility of opposite antiferromagnetic and ferromagnetic Kondo screening--the latter exhibiting a totally different and unexplored zero-bias anomaly. The present matching method between DFT and NRG should permit the quantitative understanding and exploration of this larger variety of Kondo phenomena at more general magnetic nanocontacts. PMID:19525949

Mixing Mg with Ti leads to a hydride Mg(x)Ti((1 - x))H(2) with markedly improved (de)hydrogenation properties for x ? 0.8, as compared to MgH(2). Optically thin films of Mg(x)Ti((1 - x))H(2) have a black appearance, which is remarkable for a hydride material. In this paper we study the structure and stability of Mg(x)Ti((1 - x))H(2), x = 0-1 by first-principles calculations at the level of density functional theory. We give evidence for a fluorite to rutile phase transition at a critical composition x(c) = 0.8-0.9, which correlates with the experimentally observed sharp decrease in (de)hydrogenation rates at this composition. The densities of states of Mg(x)Ti((1 - x))H(2) have a peak at the Fermi level, composed of Ti d states. Disorder in the positions of the Ti atoms easily destroys the metallic plasma, however, which suppresses the optical reflection. Interband transitions result in a featureless optical absorption over a large energy range, causing the black appearance of Mg(x)Ti((1 - x))H(2). PMID:21386386

Using interatomic potentials derived from first-principles generalized pseudopotential theory, finite-temperature phase transitions in both simple and transition metals can be studied through a combination of analytic statistical methods and molecular-dynamics simulation. In the prototype simple metal-Mg, where volume and pair forces adequately describe the energetics, a complete and accurate phase diagram has thereby been obtained to 60 GPa. A rapidly temperature-dependent hcp-bcc phase line is predicted which ends in a triple point on the melting curve near 4 GPa. In central transition metals such as Mo or Fe, on the other hand, the energetics are complicated by d-state interactions which give rise to both many-body angular forces and enhanced electron-thermal contributions. We have made a detailed study of these phenomena and their impact on melting in the prototype case of Mo and a full melting curve to 2 Mbar has been obtained. In the case of Fe, we are examining the high-pressure phase diagram and the question of whether or not there exists a high-pressure, high-temperature solid bcc phase, as has been speculated. To date, we have shown that the bcc structure is both thermodynamically and mechanically unstable at high pressure and zero temperature, with a large and increasing bcc-hcp energy difference under compression.

Gold nanoclusters have the tunable optical absorption property, and are promising for cancer cell imaging, photothermal therapy and radiotherapy. First-principle is a very powerful tool for design of novel materials. In the present work, structural properties, band gap engineering and tunable optical properties of Ag-doped gold clusters have been calculated using density functional theory. The electronic structure of a stable Au20 cluster can be modulated by incorporating Ag, and the HOMO–LUMO gap of Au20?nAgn clusters is modulated due to the incorporation of Ag electronic states in the HOMO and LUMO. Furthermore, the results of the imaginary part of the dielectric function indicate that the optical transition of gold clusters is concentration-dependent and the optical transition between HOMO and LUMO shifts to the low energy range as the Ag atom increases. These calculated results are helpful for the design of gold cluster-based biomaterials, and will be of interest in the fields of radiation medicine, biophysics and nanoscience. PMID:21686162

Gold nanoclusters have the tunable optical absorption property, and are promising for cancer cell imaging, photothermal therapy and radiotherapy. First-principle is a very powerful tool for design of novel materials. In the present work, structural properties, band gap engineering and tunable optical properties of Ag-doped gold clusters have been calculated using density functional theory. The electronic structure of a stable Au(20) cluster can be modulated by incorporating Ag, and the HOMO-LUMO gap of Au(20-) (n)Ag(n) clusters is modulated due to the incorporation of Ag electronic states in the HOMO and LUMO. Furthermore, the results of the imaginary part of the dielectric function indicate that the optical transition of gold clusters is concentration-dependent and the optical transition between HOMO and LUMO shifts to the low energy range as the Ag atom increases. These calculated results are helpful for the design of gold cluster-based biomaterials, and will be of interest in the fields of radiation medicine, biophysics and nanoscience. PMID:21686162

Firstprinciples phonon dispersion relations are reported for a range of magnetic perovskite oxides in cubic high-symmetry reference structures. Materials considered include EuTiO3 and BiFeO3. For each system, the dominant lattice instabilities are identified. These are frozen-in, singly and in combination, and the structures are optimized in the resulting space groups. From this, we identify distinct low-energy alternatives to the ground-state structure. We focus particularly on the dependence of the lattice instabilities and structural energetics of low-lying phases on the magnetic order, and extract key magnetostructural coupling parameters. The analysis is applied to predict possible structural and magnetic phase transitions as a function of epitaxial strain and/or of composition in low-concentration solid solutions (A1-xA'xBO3, AB1-xB'xO3, A1-xA'xB1-yB'yO3 for small x,y).

The lowering of the dielectric constant of Ba_xSr_1-xTiO3 (BST) films compared to bulk can be attributed, at least in part, to the effects of defects associated with film growth. In BST films grown on MgO substrates, such defects include antiphase boundaries (APBs), which have been clearly observed using electron microscopy. In this work, using a first-principles pseudopotential approach based on variational density functional pertubation theory, we have investigated the structure, lattice dynamics and dielectric properties of two relevant APBs in SrTiO3 (Sr-rich and Ti-rich) using ordered supercells. Comparison with bulk SrTiO3 shows that the Born effective charges and electronic dielectric tensor decrease and the characteristic low-frequency polar mode increases in frequency, leading to a significant lowering of the lattice contribution to the dielectric response. We suggest that this change can be understood as the result of the disruption of the Ti-O chains normal to the APB, and thus that this mechanism is also relevant to the solid solution. This work is supported by U. Maryland/Rutgers NSF-MRSEC DMR-00-80008.

The synthesis and study of soft-donor uranyl complexes can provide new insights into the coordination chemistry of non-aqueous [UO]2^+ Recently, the tunable N-donor ligand 2,6-Bis(2-benzimidazyl)pyridine (BBP) was employed to produce novel uranyl complexes in which the [UO]2^+ cation is ligated by anionic and covalent groups with discrete chemical differences. In this work we investigate the electronic structure of the three such uranyl-BBP complexes via near-edge X-ray absorption fine structure (NEXAFS) experiments and simulations using the eXcited electron and Core-Hole (XCH) approach [1]. The evolution of the structural as well as electronic properties across the three complexes is studied systematically. Computed N K-edge and O K-edge NEXAFS spectra are compared with experiment and spectral features assigned to specific electronic transitions in these complexes. Studying the variations in spectral features arising from N K-edge absorption provides a clear picture of ligand-uranyl bonding in these systems. References: [1] D. Prendergast and G. Galli, X-ray absorption spectra of water from first-principles calculations, Phys. Rev. Lett., 215502 (2006).

Using a generalized genetic algorithm, we propose four new sp(3) carbon allotropes with 5-6-7 (5-6-7-type Z-ACA and Z-CACB) or 4-6-8 (4-6-8-type Z4-A(3)B(1) and A4-A(2)B(2)) carbon rings. Their stability, mechanical and electronic properties are systematically studied using a first-principles method. We find that the four new carbon allotropes show amazing stability in comparison with the carbon phases proposed recently. Both 5-6-7-type Z-ACA and Z-CACB are direct band-gap semiconductors with band gaps of 2.261 eV and 4.196 eV, respectively. However, the 4-6-8-type Z4-A(3)B(1) and A4-A(2)B(2) are indirect band-gap semiconductors with band gaps of 3.105 eV and 3.271 eV, respectively. Their mechanical properties reveal that all the four carbon allotropes proposed in present work are superhard materials, which are comparable to diamond. PMID:22576111

Atomic and electronic structures of intrinsic point defects in yttrium oxysulfides (Y2O2S) are studied by first-principles total-energy calculations based on density-functional theory combined with normconserving pseudopotentials. Energetics of all the intrinsic point defects are determined for a variety of charge states. From the energetics, the concentrations of the anion vacancies and the interstitial anions are found to be larger than those of the yttrium vacancy and the interstitial yttrium atom under practical conditions. It is also found that the oxygen vacancy, the sulfur vacancy, and the interstitial sulfur atom induce relatively deep levels in the energy gap, whereas the interstitial oxygen atom induces relatively shallow acceptor levels. These findings are consistent with observed broad-band blue luminescence in undoped yttrium oxysulfide, existence of shallow acceptor levels in oxysulfides, and are presumably related to persistent phosphorescence and energy storage phenomena in Eu-doped oxysulfides. Furthermore, negative-U characters are found in the oxygen vacancy and the interstitial sulfur. These behaviors of the defects can be explained from the viewpoint of the covalent bonds newly appearing around the defects in the ionic host material.

The Material Control and Accountability (MC&A) program at the Nevada Test Site (NTS) was selected as a test bed for the Safeguards FirstPrinciples Initiative (SFPI). The implementation of the SFPI is evaluated using the system effectiveness model and the program is managed under an approved MC&A Plan. The effectiveness model consists of an evaluation of the critical elements necessary to detect, deter, and/or prevent the theft or diversion of Special Nuclear Material (SNM). The modeled results indicate that the MC&A program established under this variance is still effective, without creating unacceptable risk. Extensive performance testing is conducted through the duration of the pilot to ensure the protection system is effective and no material is at an unacceptable risk. The pilot was conducted from January 1, 2007, through May 30, 2007. This paper will discuss the following activities in association with SFPI: 1. Development of Timeline 2. Crosswalk of DOE Order and SFPI 3. Peer Review 4. Deviation 5. MC&A Plan and Procedure changes 6. Changes implemented at NTS 7. Training 8. Performance Test

We have used a first-principles ultra-soft-pseudopotential method in conjunction with an efficient preconditioned conjugate-gradient scheme to investigate the properties of a series of eight cubic perovskite compounds. The materials considered in this study are BaTiO3, SrTiO3, CaTiO3, KNbO3, NaNbO3 PbTiO3 , PbZrO3, and BaZrO3. We computed the total-energy surface for zone-center distortions correct to fourth order in the soft-mode displacement, including renormalizations due to strain coupling. Quantities calculated for each material include lattice constants, elastic constants, zone-center phonon frequencies, Grüneisen parameters, and band structures. Our calculations correctly predict the symmetry of the ground-state structures of all compounds whose observed low-temperature structure retains a primitive five-atom unit cell. The database of results we have generated shows a number of trends which can be understood using simple chemical ideas based on the sizes of ions, and the frustration inherent in the cubic perovskite structure.

The cytochrome P450 superfamily of enzymes is of enormous interest in the biological sciences due to the wide range of endogenous and xenobiotic compounds which it metabolises, including many drugs. We describe the use of firstprinciples quantum mechanical modeling techniques, based on density functional theory, to determine the outcome of interactions between an enzyme and a number of compounds. Specifically, we calculate the spin state of an Fe3+ ion present in a haem moiety at the active site of these enzymes. The spin state of this ion indicates if the catalytic reaction will proceed. The computational results obtained compare favorably with experimental data. Only the principle components of the active site of the enzyme are included in the computational models, demonstrating that only a small fragment of the protein needs to be included in the models in order to accurately reproduce this aspect of the enzymes' function. These results open the way for further investigation of this superfamily of enzymes using the methods detailed in this paper.

We perform a first-principles density functional theory study on structural and electronic properties of a sery of crystal-phase heterostructure atomic-scale superlattice (SL) nanowires (NW) from GaN material, i.e. GaN wurtzite(WZ) /zincblende (ZB) material interface. The effects of surface/interface relaxation and surface stress which are absent in atomistic models are carefully taken into account. Structural properties, energy bands and electronic properties for a class of hexagonal wires with various period of SL structure and diameter size are discussed. Pseudo hydrogen atoms, i.e. hydrogen with partial charges, are used to passivate the dangling surface bonds, which remove the localized in-gap surface states and suppress the surface reconstructions. With this passivation procedure the band structure show the type II for all wires. While the electrical aspects of these SL nanowires are explored through density functional theory, their subsequent band structures are used to determine the thermoelectric properties via the Boltzmann transport theory. Finally, the thermoelectric propertys dependence on temperature is unveiled.

The magnesium (Mg) phase characterized within Mg/Nb multilayers can adopt either a body-centered cubic (bcc-Mg) or hexagonal close packed (hcp-Mg) structure, depending on the Mg layer thickness. Using first-principles density functional theory, we find that bcc-Mg has a similar weight density of hcp-Mg, lower Young's modulus, and higher shear modulus than hcp-Mg, and the same conventional slip systems as the bcc structure. A simple theoretical model is developed to predict the structural stability of both the bcc-Mg/Nb and hcp-Mg/Nb multilayers. It shows that the bcc-Mg/Nb multilayer is energetically favorable when the bcc-Mg layer is less than 4.2 nm.

We present a firstprinciplestheoretical framework that accurately accounts for several properties of ice, over a wide pressure range. In particular, we show that, by using a recently developed nonlocal van der Waals functional and by taking into account hydrogen zero point motion, one can properly describe the zero temperature equation of state, the vibrational spectra, and the dielectric properties of ice at low pressure and of ice VIII, a stable phase between 2 and 60 GPa. While semilocal density functionals yield a transition pressure from ice XI to VIII that is overestimated by almost an order of magnitude, we find good agreement with experiments when dispersion forces are taken into account. Zero point energy contributions do not alter the computed transition pressure, but they affect structural properties, including equilibrium volumes and bulk moduli.

Copper based catalysts are of importance to a number of industrial processes including the synthesis of methanol, the reduction and decomposition of nitrogen oxides, and treatment of waste water. In copper catalysis surface oxidation and oxidic overlayers are believed to play a crucial role. In this work using density functional theory (DFT) within the generalized gradient approximation (GGA) we have studied the stability and associated electronic properties of the oxidized Cu(100) and Cu(110) surfaces. Especially, we have focused on studies of changes in the interlayer spacing, electron work function, binding energy, and density of states with oxygen coverage. We have examined the cases of various oxygen coverages of the non-reconstructed, missing row reconstructed Cu(100), and added row reconstructed Cu (110) surfaces. The first-principles calculations in this work have been performed using DMOl3 code. The obtained theoretical results have been compared with available experimental data.

The electronic, structural, mechanical and superconducting properties of group VB mononitrides are investigated by means of firstprinciples calculation based on density functional theory with generalized gradient approximation. The calculated ground state properties are in good agreement with previous experimental and theoretical results. Among the three crystallographic structures that have been investigated, the hexagonal WC phase is found to more stable than the cubic ones. Under high pressure, a series of structural phase transition from WC ? NaCl ? CsCl phase is also predicted in VN, NbN and TaN. The calculated elastic constants indicate that all the three nitrides are mechanically stable at ambient pressure. The estimated Zener ratio and linear compressibility coefficients Kc/Ka reveals that these materials exhibit elastic anisotropy. The estimated superconducting transition temperature (Tc) values as a function of pressure for VN, NbN and TaN are 35.5, 37.5 and 30.5 K respectively.

In the frame of density functional theory, first-principles calculations have been carried out to investigate the structures, elastic constants, structural phase transition between B1 and B2 phases and thermodynamic properties of the zirconium nitride (ZrN) by means of the generalized gradient approximation. The equilibrium lattice parameter we obtained for ZrN in B1 phase is closer to the experiment results than previous theoretical results. In addition, the calculations of the elastic constants show that ZrN is a brittle material. What is more, based on third-order natural strain equation of state, the phase transition pressure 338 GPa for ZrN is predicted for B1-B2 transition. According to the quasi-harmonic Debye model, the thermodynamic parameters of ZrN have been investigated systematically.

Forming a chemically stable low-resistance back contact for CdTe thin-film solar cells is critically important to the cell performance. This paper reports theoretical study of the effects of the back-contact material, Sb{sub 2}Te{sub 3}, on the performance of the CdTe solar cells. First-principles calculations show that Sb impurities in p-type CdTe are donors and can diffuse with low diffusion barrier. There properties are clearly detrimental to the solar-cell performance. The Sb segregation into the grain boundaries may be required to explain the good efficiencies for the CdTe solar cells with Sb{sub 2}Te{sub 3} back contacts.

Lithium is one of the simplest metals, with negative charge carriers and a close reproduction of free-electron dispersion. Experimentally, however, Li is one of a handful of elemental solids (along with Cu, Ag, and Au) where the sign of the Seebeck coefficient (S) is opposite to that of the carrier. This counterintuitive behavior still lacks a satisfactory interpretation. We calculate S fully from firstprinciples, within the framework of Allen's formulation of Boltzmann transport theory. Here it is crucial to avoid the constant relaxation time approximation, which gives a sign for S which is necessarily that of the carriers. Our calculated S are in excellent agreement with experimental data, up to the melting point. In comparison with another alkali metal, Na, we demonstrate that within the simplest nontrivial model for the energy dependency of the electron lifetimes, the rapidly increasing density of states (DOS) across the Fermi energy is related to the sign of S in Li. The exceptional energy dependence of the DOS is beyond the free-electron model, as the dispersion is distorted by the Brillouin zone edge; this has a stronger effect in Li than other alkali metals. The electron lifetime dependency on energy is central, but the details of the electron-phonon interaction are found to be less important, contrary to what has been believed for several decades. Band engineering combined with the mechanism exposed here may open the door to new "ambipolar" thermoelectric materials, with a tunable sign for the thermopower even if either n- or p-type doping is impossible.

Purpose: To develop an algorithm for computing realistic digitally reconstructed radiographs (DRRs) that match real cone-beam CT (CBCT) projections with no artificial adjustments. Methods: The authors used measured attenuation data from cone-beam CT projection radiographs of different materials to obtain a function to convert CT number to linear attenuation coefficient (LAC). The effects of scatter, beam hardening, and veiling glare were first removed from the attenuation data. Using this conversion function the authors calculated the line integral of LAC through a CT along rays connecting the radiation source and detector pixels with a ray-tracing algorithm, producing raw DRRs. The effects of scatter, beam hardening, and veiling glare were then included in the DRRs through postprocessing. Results: The authors compared actual CBCT projections to DRRs produced with all corrections (scatter, beam hardening, and veiling glare) and to uncorrected DRRs. Algorithm accuracy was assessed through visual comparison of projections and DRRs, pixel intensity comparisons, intensity histogram comparisons, and correlation plots of DRR-to-projection pixel intensities. In general, the fully corrected algorithm provided a small but nontrivial improvement in accuracy over the uncorrected algorithm. The authors also investigated both measurement- and computation-based methods for determining the beam hardening correction, and found the computation-based method to be superior, as it accounted for nonuniform bowtie filter thickness. The authors benchmarked the algorithm for speed and found that it produced DRRs in about 0.35 s for full detector and CT resolution at a ray step-size of 0.5 mm. Conclusions: The authors have demonstrated a DRR algorithm calculated from firstprinciples that accounts for scatter, beam hardening, and veiling glare in order to produce accurate DRRs. The algorithm is computationally efficient, making it a good candidate for iterative CT reconstruction techniques that require a data fidelity term based on the matching of DRRs and projections. PMID:23298093

In this paper we used a general stochastic processes framework to derive from firstprinciples the incidence rate function that characterizes epidemic models. We investigate a particular case, the Liu-Hethcote-van den Driessche's (LHD) incidence rate function, which results from modeling the number of successful transmission encounters as a pure birth process. This derivation also takes into account heterogeneity in the population with regard to the per individual transmission probability. We adjusted a deterministic SIRS model with both the classical and the LHD incidence rate functions to time series of the number of children infected with syncytial respiratory virus in Banjul, Gambia and Turku, Finland. We also adjusted a deterministic SEIR model with both incidence rate functions to the famous measles data sets from the UK cities of London and Birmingham. Two lines of evidence supported our conclusion that the model with the LHD incidence rate may very well be a better description of the seasonal epidemic processes studied here. First, our model was repeatedly selected as best according to two different information criteria and two different likelihood formulations. The second line of evidence is qualitative in nature: contrary to what the SIRS model with classical incidence rate predicts, the solution of the deterministic SIRS model with LHD incidence rate will reach either the disease free equilibrium or the endemic equilibrium depending on the initial conditions. These findings along with computer intensive simulations of the models' Poincaré map with environmental stochasticity contributed to attain a clear separation of the roles of the environmental forcing and the mechanics of the disease transmission in shaping seasonal epidemics dynamics. PMID:21379320

The Department of Energy`s Office of Environmental Restoration and Waste Management (EM) faces a challenging mission. To increase efficiency, EM is undertaking a number of highly innovative initiatives--two of which are of particular importance to the present study. One is the 2006 Plan, a planning and budgeting process that seeks to convert the clean-up program from a temporally and fiscally open-ended endeavor to a strictly bounded one, with firm commitments over a decade-long horizon. The second is a major overhauling of the management and contracting practices that define the relationship between the Department and the private sector, aimed at cost reduction by increasing firms` responsibilities and profit opportunities and reducing DOE`s direct participation in management practices and decisions. The goal of this paper is to provide an independent perspective on how EM should create new management practices to deal with private sector partners that are motivated by financial incentives. It seeks to ground this perspective in real world concerns--the background of the clean-up effort, the very difficult technical challenges it faces, the very real threats to environment, health and safety that have now been juxtaposed with financial drivers, and the constraints imposed by government`s unique business practices and public responsibilities. The approach is to raise issues through application of firstprinciples. The paper is targeted at the EM policy officer who must implement the joint visions of the 2006 plan and privatization within the context of the tradeoff between terminal risk reduction and interim risk management.

The structure, energetics, electronic, and optical properties of the organic molecule, diindenoperylene (DIP), are investigated by first-principles density-functional and time-dependent density-functional theory. The photoabsorption cross section, computed on the optimized geometry within the linear response theory, gives results in good agreement with experimental data, with minor differences ascribed to vibrational levels and to solvent effects. Ab initio dynamical simulations of the molecular triplet excited state show that DIP is stable against distortions, at least on the picosecond time scale. The theoretical approach, involving a combination of first-principles techniques, is shown to be able to describe in detail the response properties of low-dimensional organic semiconductor systems, currently important in nanotechnological applications.

Fe-bearing clay minerals serve as an important source and sink for electrons in redox reactions in various subsurface geochemical environments, and electron transfer (ET) properties of the Fe2+/Fe3+ redox couple play a decisive role in a variety of physicochemical processes involving clays. Here, we apply first-principles calculations using both periodic GGA+U planewave and Hartree-Fock molecular-cluster frameworks in conjuction with small polaron hopping approach and Marcus electron transfer theory to examine electron exchange mobilities in an Fe-rich smectite, taking nontronite as a case study. GGA+U calculations of the activation barrier for small-polaron migration provide rates of electron hopping that agree very well with values deduced from variable temperature Mössbauer data (M. V. Schaefer, et. al., Environ. Sci. Technol. 45, 540, (2011)), indicating a surprisingly fast electron mobility at room temperature. Based on molecular cluster calculations, we show that the state with tetrahedral Fe2+ ion in the nontronite lattice is about 0.9 eV higher than the one with octahedral Fe2+. Also, evaluation of the ET rates for the Fe2+/Fe3+ electron hopping in tetrahedral (TS) and octahedral sheets (OS), as well as across the sheets (TS–OS) shows that the dominant contribution to the bulk electronic conductivity should come from the ET within the OS. Deprotonation of structural OH groups mediating ET between the Fe ions in the OS is found to decrease the internal reorganization energy and to increase the magnitude of the electronic coupling matrix element, whereas protonation (to OH2 groups) has the opposite effect. Overall, our calculations suggest that the major factors affecting ET rates are the nature and structure of the nearest-neighbor local environment and the degree of covalency of the bonds between Fe and ligands mediating electron hops. The generally higher reorganization energy and weaker electronic coupling found in Fe-bearing clay minerals leads to electron mobilities much lower than in iron oxides.

ABINIT [ http://www.abinit.org] allows one to study, from first-principles, systems made of electrons and nuclei (e.g. periodic solids, molecules, nanostructures, etc.), on the basis of Density-Functional Theory (DFT) and Many-Body Perturbation Theory. Beyond the computation of the total energy, charge density and electronic structure of such systems, ABINIT also implements many dynamical, dielectric, thermodynamical, mechanical, or electronic properties, at different levels of approximation. The present paper provides an exhaustive account of the capabilities of ABINIT. It should be helpful to scientists that are not familiarized with ABINIT, as well as to already regular users. First, we give a broad overview of ABINIT, including the list of the capabilities and how to access them. Then, we present in more details the recent, advanced, developments of ABINIT, with adequate references to the underlying theory, as well as the relevant input variables, tests and, if available, ABINIT tutorials. Program summaryProgram title: ABINIT Catalogue identifier: AEEU_v1_0 Distribution format: tar.gz Journal reference: Comput. Phys. Comm. Programming language: Fortran95, PERL scripts, Python scripts Computer: All systems with a Fortran95 compiler Operating system: All systems with a Fortran95 compiler Has the code been vectorized or parallelized?: Sequential, or parallel with proven speed-up up to one thousand processors. RAM: Ranges from a few Mbytes to several hundred Gbytes, depending on the input file. Classification: 7.3, 7.8 External routines: (all optional) BigDFT [1], ETSF IO [2], libxc [3], NetCDF [4], MPI [5], Wannier90 [6] Nature of problem: This package has the purpose of computing accurately material and nanostructure properties: electronic structure, bond lengths, bond angles, primitive cell size, cohesive energy, dielectric properties, vibrational properties, elastic properties, optical properties, magnetic properties, non-linear couplings, electronic and vibrational lifetimes, etc. Solution method: Software application based on Density-Functional Theory and Many-Body Perturbation Theory, pseudopotentials, with planewaves, Projector-Augmented Waves (PAW) or wavelets as basis functions. Running time: From less than one second for the simplest tests, to several weeks. The vast majority of the >600 provided tests run in less than 30 seconds. References:[1] http://inac.cea.fr/LSim/BigDFT. [2] http://etsf.eu/index.php?page=standardization. [3] http://www.tddft.org/programs/octopus/wiki/index.php/Libxc. [4] http://www.unidata.ucar.edu/software/netcdf. [5] http://en.wikipedia.org/wiki/MessagePassingInterface. [6] http://www.wannier.org.

The absence of a direct-to-indirect band gap transition in ReS2 when going from the monolayer to bulk makes it special among the other semiconducting transition metal dichalcogenides. The functionalization of this promising layered material emerges as a necessity for the next generation technological applications. Here, the structural, electronic, and magnetic properties of substitutionally doped ReS2 monolayers at either the S or Re site were systematically studied by using firstprinciples density functional calculations. We found that substitutional doping of ReS2 depends sensitively on the growth conditions of ReS2. Among the large number of non-metallic atoms, namely H, B, C, Se, Te, F, Br, Cl, As, P, and N, we identified the most promising candidates for n-type and p-type doping of ReS2. While Cl is an ideal candidate for n-type doping, P appears to be the most promising candidate for p-type doping of the ReS2 monolayer. We also investigated the doping of ReS2 with metal atoms, namely Mo, W, Ti, V, Cr, Co, Fe, Mn, Ni, Cu, Nb, Zn, Ru, Os and Pt. Mo, Nb, Ti, and V atoms are found to be easily incorporated in a single layer of ReS2 as substitutional impurities at the Re site for all growth conditions considered in this work. Tuning chemical potentials of dopant atoms energetically makes it possible to dope ReS2 with Fe, Co, Cr, Mn, W, Ru, and Os at the Re site. We observe a robust trend for the magnetic moments when substituting a Re atom with metal atoms such that depending on the electronic configuration of dopant atoms, the net magnetic moment of the doped ReS2 becomes either 0 or 1 ?B. Among the metallic dopants, Mo is the best candidate for p-type doping of ReS2 owing to its favorable energetics and promising electronic properties. PMID:25001566

Conspectus A ferroelectric crystal exhibits macroscopic electric dipole or polarization arising from spontaneous ordering of its atomic-scale dipoles that breaks inversion symmetry. Changes in applied pressure or electric field generate changes in electric polarization in a ferroelectric, defining its piezoelectric and dielectric properties, respectively, which make it useful as an electromechanical sensor and actuator in a number of applications. In addition, a characteristic of a ferroelectric is the presence of domains or states with different symmetry equivalent orientations of spontaneous polarization that are switchable with large enough applied electric field, a nonlinear property that makes it useful for applications in nonvolatile memory devices. Central to these properties of a ferroelectric are the phase transitions it undergoes as a function of temperature that involve lowering of the symmetry of its high temperature centrosymmetric paraelectric phase. Ferroelectricity arises from a delicate balance between short and long-range interatomic interactions, and hence the resulting properties are quite sensitive to chemistry, strains, and electric charges associated with its interface with substrate and electrodes. First-principles density functional theoretical (DFT) calculations have been very effective in capturing this and predicting material and environment specific properties of ferroelectrics, leading to fundamental insights into origins of ferroelectricity in oxides and chalcogenides uncovering a precise picture of electronic hybridization, topology, and mechanisms. However, use of DFT in molecular dynamics for detailed prediction of ferroelectric phase transitions and associated temperature dependent properties has been limited due to large length and time scales of the processes involved. To this end, it is quite appealing to start with input from DFT calculations and construct material-specific models that are realistic yet simple for use in large-scale simulations while capturing the relevant microscopic interactions quantitatively. In this Account, we first summarize the insights obtained into chemical mechanisms of ferroelectricity using first-principles DFT calculations. We then discuss the principles of construction of first-principles model Hamiltonians for ferroelectric phase transitions in perovskite oxides, which involve coarse-graining in time domain by integrating out high frequency phonons. Molecular dynamics simulations of the resulting model are shown to give quantitative predictions of material-specific ferroelectric transition behavior in bulk as well as nanoscale ferroelectric structures. A free energy landscape obtained through coarse-graining in real-space provides deeper understanding of ferroelectric transitions, domains, and states with inhomogeneous order and points out the key role of microscopic coupling between phonons and strain. We conclude with a discussion of the multiscale modeling strategy elucidated here and its application to other materials such as shape memory alloys. PMID:25361389

Firstprinciples total energy calculations on hcp, ? (a three atom simple hexagonal), ? (bcc) and fcc phases of osmium have been performed as a function of hydrostatic compression employing the FP-LAPW method. The comparison of total energies of these phases up to a maximum compression V/V(0) = 0.58 (pressure?700 GPa) shows that the hcp structure remains stable up to this compression. The 300 K isotherm is determined after adding finite temperature thermal contributions to the total energy calculated as a function of volume at 0 K. From the theoretically determined isotherm, we have derived the shock Hugoniot of this metal and determined the shock parameters C(0) and s to be 4.48 km s(-1) and 1.32, respectively. Employing the theoretically calculated Gruneisen parameter in the differential form of the Lindemann melting rule, we have determined the variation of melting point of the osmium with pressure. The theoretically derived melting curve and the temperature rise along the Hugoniot predict the shock melting of osmium at ?447 GPa with a corresponding temperature of ?9203 K. PMID:21693986

The authors report on theoretical calculations of interlayer exchange coupling between two Fe layers separated by a modified Cu spacer. These calculations were motivated by experimental investigations of similar structures by the SFU group. The multilayer structures of interest have the general form: Fe/Cu(k)/Fe and Fe/Cu(m)/X(1)/Cu(n)/Fe where X indicates one AL (atomic layer) of foreign atoms X (Cr, Ag, or Fe) and k, m, n represent the number of atomic layers of Cu. The purpose of the experimental and theoretical work was to determine the effect of modifying the pure Cu spacer by replacing the central Cu atomic layer with the atomic layer of foreign atoms X. The firstprinciples calculation were performed using the Layer Korringa-Kohn-Rostoker (LKKR) method. The theoretical thickness dependence of the exchange coupling between two semi-infinite Fe layers was calculated for pure Cu spacer thicknesses in the range of 0 < k < 16. The effect of the foreign atoms X on the exchange coupling was investigated using the structure with 9 AL Cu spacer as a reference sample. The calculated changes in the exchange coupling are in qualitative agreement with experiment.

The development of high efficiency organic photovoltaics (OPV) has recently become enabled by the synthesis of new conjugated polymers with low band gap that allow light absorption over a broader range of the spectrum. Stability of these new polymers, a key requirement for commercialization, has not yet received sufficient attention. Here, we report first-principlestheoretical modeling of photo-induced degradation of OPV polymers carried out using ab-initio density functional theory (DFT). We report photooxidation routes and reaction products for reactive species including superoxide oxygen anions and hydroxyl groups interacting with the standard workhorse OPV polymer, poly(3-hexyl-thiophene) (P3HT). We discuss theoretical issues and challenges affecting the modeling such reactions in OPV polymers. We also discuss the application of theoretical methods to low-band-gap polymers, and in particular, the effect of the chemical substitution on the photoexcitation properties of these new polymers. Sandia National Laboratories is a multiprogram laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Deparment of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

We present a simple theoretical model for the emission from double pulse laser-induced plasmas that was developed to better understand the processes and factors involved in enhancement of plasma emission. In this model, the plasma emission is directly proportional to the square of plasma density, its volume, and the fraction of second laser pulse absorbed through inverse bremsstrahlung absorption by the plasma plume of the first laser pulse. The electron-ion collision frequency determines the profile and location of the peak of emission enhancement with respect to the delay between the two lasers, whereas the amplitude of the enhancement is mainly dependent on the increase in the mass ablation rate after the second laser pulse. The effects of increase in temperature and in plasma volume after the second laser pulse are also discussed in light of this model. PMID:19122700

Using calculations from firstprinciples based on density-functional theory we have studied the strain sensitivity of the A15 superconductor Nb3Sn. The Nb3Sn lattice cell was deformed in the same way as observed experimentally on multifilamentary, technological wires subject to loads applied along their axes. The phonon dispersion curves and electronic band structures along different high-symmetry directions in the Brillouin zone were calculated, at different levels of applied strain, ?, on both the compressive and the tensile side. Starting from the calculated averaged phonon frequencies and electron-phonon coupling, the superconducting characteristic critical temperature of the material, Tc, has been calculated by means of the Allen-Dynes modification of the McMillan formula. As a result, the characteristic bell-shaped Tc versus ? curve, with a maximum at zero intrinsic strain, and with a slight asymmetry between the tensile and compressive sides, has been obtained. These first-principle calculations thus show that the strain sensitivity of Nb3Sn has a microscopic and intrinsic origin, originating from shifts in the Nb3Sn critical surface. In addition, our computations show that variations of the superconducting properties of this compound are correlated to stress-induced changes in both the phononic and electronic properties. Finally, the strain function describing the strain sensitivity of Nb3Sn has been extracted from the computed Tc(?) curve, and compared to experimental data from multifilamentary, composite wires. Both curves show the expected bell-shaped behavior, but the strain sensitivity of the wire is enhanced with respect to the theoretical predictions for bulk, perfectly binary and stoichiometric Nb3Sn. An understanding of the origin of this difference might open potential pathways towards improvement of the strain tolerance in such systems.

In this study, equilibrium mass-dependent isotopic fractionation among representative Te-bearing species is estimated with first-principles thermodynamic calculations. Tellurium is a group 16 element (along with O, S, and Se) with eight stable isotopes ranging in mass from 120Te to 130Te, and six commonly-occurring oxidation states: -II, -I, 0, +II, +IV, and +VI. In its reduced form, Te(-II), tellurium has a unique crystal-chemical role as a bond partner for gold and silver in epithermal and orogenic gold deposits, which likely form when oxidized Te species (e.g., H2TeO3, TeO32-) or perhaps polytellurides (e.g., Te22-) interact with precious metals in hydrothermal solution. Te(IV) is the most common oxidation state at the Earth's surface, including surface outcrops of telluride ore deposits, where tellurite and tellurate minerals form by oxidation. In the ocean, dissolved tellurium tends to be scavenged by particulate matter. Te(VI) is more abundant than Te(IV) in the ocean water (1), even though it is thought to be less stable thermodynamically. This variety of valence states in natural systems and range of isotopic masses suggest that tellurium could exhibit geochemically useful isotope abundance variations. Tellurium isotope fractionations were determined for representative molecules and crystals of varying complexity and chemistry. Gas-phase calculations are combined with supermolecular cluster models of aqueous and solid species. These in turn are compared with plane-wave density functional theory calculations with periodic boundary conditions. In general, heavyTe/lightTe is predicted to be higher for more oxidized species, and lower for reduced species, with 130Te/125Te fractionations as large as 4‰ at 100?C between coexisting Te(IV) and Te(-II) or Te(0) compounds. This is a much larger fractionation than has been observed in naturally occurring redox pairs (i.e., Te (0) vs. Te(IV) species) so far, suggesting that disequilibrium processes may control oxidation and reduction. Se- and S-isotope redox systems also show kinetically-controlled isotopic disequilibrium, and may serve as useful analogues. Among Te(-II) species, fractionations are smaller (< 1‰ at 100?C). (Au,Ag)Te2 minerals (calaverite, krennerite) and (Au,Ag)2Te minerals (petzite, hessite) are expected to have similar isotopic compositions to vapor-phase H2Te, and there appears to be little discernable effect from Ag,Au solid solution. Altaite (PbTe) will have somewhat lower 130Te/125Te. Calculated fractionation factors for gas-phase species like H2Te and TeF6, based on hybrid density functional theory (B3LYP), agree well with earlier estimates (2). For telluride-bearing crystals, cluster models are in qualitative agreement with periodic boundary condition calculations, especially when larger basis sets (e.g., aug-cc-PVDZ-PP) are used; however, cluster models tend to predict higher 130Te/125Te for reasons that are not yet clear. References: 1. Hein et al. (2003) GCA 67:6. 2. Smithers et al. (1968) Can. J. Chem. 46:4.

We investigated band offsets at Cu2ZnSnS4(CZTS)/CdS and CdS/ZnO interfaces in a typical CZTS/CdS/ZnO heterojunction solar cell by combining x-ray photoelectron spectroscopy and optical absorption spectroscopy as well as first-principles calculations. X-ray photoelectron spectroscopy and optical absorption spectroscopy measurements indicate that the conduction-band offsets at both CZTS/CdS and CdS/ZnO interfaces show type-II alignment with values of 0.13 eV and 1.00 eV, respectively, which are well supported by first-principles calculations based on the hybrid functional method. Our results suggest that, although type-II alignment for CZTS/CdS heterojunction can form less of a barrier to electron transport across the interfaces, the narrowing of the ‘interface bandgap’ increases recombination of carriers.

Density-functional electronic-structure calculations have been used to investigate the ambient pressure and low temperature elastic properties of the ground-state {alpha} phase of plutonium metal. The electronic structure and correlation effects are modeled within a fully relativistic antiferromagnetic treatment with a generalized gradient approximation for the electron exchange and correlation functional. The 13 independent elastic constants, for the monoclinic {alpha}-Pu system, are calculated for the observed geometry. A comparison of the results with measured data from recent resonant ultrasound spectroscopy for a cast sample is made.

Density-functional electronic structure calculations have been used to investigate the ambient pressure and low temperature elastic properties of the ground-state {alpha} phase of plutonium metal. The electronic structure and correlation effects are modeled within a fully relativistic anti-ferromagnetic treatment with a generalized gradient approximation for the electron exchange and correlation functionals. The 13 independent elastic constants, for the monoclinic {alpha}-Pu system, are calculated for the observed geometry. A comparison of the results with measured data from resonant ultrasound spectroscopy for a cast sample is made.

Hole transfer processes between base pairs in natural DNA and size-expanded DNA (xDNA) are studied and compared, by means of an accurate firstprinciples evaluation of the effective electronic couplings (also known as transfer integrals), in order to assess the effect of the base augmentation on the efficiency of charge transport through double-stranded DNA. According to our results, the size expansion increases the average electronic coupling, and thus the CT rate, with potential implications in molecular biology and in the implementation of molecular nanoelectronics. Our analysis shows that the effect of the nucleobase expansion on the charge-transfer (CT) rate is sensitive to the sequence of base pairs. Furthermore, we find that conformational variability is an important factor for the modulation of the CT rate. From a theoretical point of view, this work offers a contribution to the CT chemistry in ?-stacked arrays. Indeed, we compare our methodology against other standard computational frameworks that have been adopted to tackle the problem of CT in DNA, and unravel basic principles that should be accounted for in selecting an appropriate theoretical level. PMID:19537767

We examine the predictive capabilities of first-principlestheoretical methods to calculate the phonon- and impurity-limited electron mobilities for a number of technologically relevant two-dimensional materials in comparison to experiment. The studied systems include perfect graphene, graphane, germanane and MoS2, as well as graphene with vacancies, and hydrogen, gold, and platinum adsorbates. We find good agreement with experiments for the mobilities of graphene (? = 2 × 105 cm2 V?1s?1) and graphane (? = 166 cm2 V?1s?1) at room temperature. For monolayer MoS2 we obtain ? = 225 cm2 V?1s?1. This value is higher than what is observed experimentally (0.5–200 cm2 V?1s?1) but is on the same order of magnitude as other recent theoretical results. For bulk MoS2 we obtain ? = 48 cm2 V?1s?1. We obtain a very high mobility of 18 200 cm2 V?1s?1 for single-layer germanane. The calculated reduction in mobility from the different impurities compares well to measurements where experimental data are available, demonstrating that the proposed method has good predictive capabilities and can be very useful for validation and materials design.

Point defects engineering in a new type hetero bilayer consisting of graphene and hexagonal boron-nitrogen (h-BN) sheet, including vacancy, substitutional C/B/N doping and the possible combinations of the former two, was theoretically studied using first-principles calculations. The optimized geometry, formation energy, magnetic moment, and electronic property of these systems are discussed. It was found that N vacancy is more likely to form than B vacancy in graphene/h-BN bilayer and their electronic properties exhibit n-type and p-type conductivity, respectively. Divacancy of N and C in hetero bilayer shows high stability and induces direct band gap in up and down spin, respectively. Combined by N substitutional doping in graphene and B vacancy in h-BN layer, this substitution-vacancy combination shows low formation energy and changes the semiconductor property of pristine graphene/h-BN bilayer to metallic. In contrast, the graphene/h-BN bilayer with the combinated defect of C-substitution in B site and C vacancy in graphene shows half-metallic electronic property. The calculated magnetic moments are in reasonable agreement with the available theoretical analysis on atomic charge distribution. This work reveals that the electronic and magnetic properties of graphene/h-BN bilayer can be effectively tuned by above proposed point defects engineering.

Enthalpies of formation of magnesium compounds from first-principles calculations Hui Zhang t An energetics database of binary magnesium compounds has been developed from first-principles calculations. Introduction Magnesium alloys are of great importance to the industrial world. With a density of 1.741 g/cm3

Firstprinciples simulations of Li ion migration in materials related to LiPON electrolytes Y. A electrolytes, we have carried out firstprinciples calculations of several related crystalline materials. Sim state film electrolyte LiPON, developed at Oak Ridge National Laboratory,[1, 2] is the most widely used

Mechanisms of Li+ diffusion in crystalline - and -Li3PO4 electrolytes from firstprinciples Yaojun electrolytes for use in batteries and related technologies. We have used first-principles modeling techniques diffusion mechanisms in idealized crystals of the electrolyte material Li3PO4 in both the and crystalline

We examine theoretically the Casimir effect between a metallic plate and several types of magnetic metamaterials in pursuit of Casimir repulsion, by employing a rigorous multiple-scattering theory for the Casimir effect. We first examine metamaterials in the form of two-dimensional lattices of inherently nonmagnetic spheres such as spheres made from materials possessing phonon-polariton and exciton-polariton resonances. Although such systems are magnetically active in infrared and optical regimes, the force between finite slabs of these materials and metallic slabs is plainly attractive since the effective electric permittivity is larger than the magnetic permeability for the studied spectrum. When lattices of magnetic spheres made from superparamagnetic composites are employed, we achieve not only Casimir repulsion but almost total suppression of the Casimir effect itself in the micrometer scale. PMID:19792414

We examine theoretically the Casimir effect between a metallic plate and several types of magnetic metamaterials in pursuit of Casimir repulsion, by employing a rigorous multiple-scattering theory for the Casimir effect. We first examine metamaterials in the form of two-dimensional lattices of inherently nonmagnetic spheres such as spheres made from materials possessing phonon-polariton and exciton-polariton resonances. Although such systems are magnetically active in infrared and optical regimes, the force between finite slabs of these materials and metallic slabs is plainly attractive since the effective electric permittivity is larger than the magnetic permeability for the studied spectrum. When lattices of magnetic spheres made from superparamagnetic composites are employed, we achieve not only Casimir repulsion but almost total suppression of the Casimir effect itself in the micrometer scale.

In this article, we present a comprehensive theoretical study of solubilities of alkali (Li, Na, K, Rb, Cs) and alkaline-earth (Be, Ca, Sr, Ba) metals in the boron-rich Mg-B system. The study is based on first-principles calculations of solutes formation energies in MgB2 , MgB4 , MgB7 alloys and subsequent statistical-thermodynamical evaluation of solubilities. The advantage of the approach consists in considering all the known phase boundaries in the ternary phase diagram. Substitutional Na, Ca, and Li demonstrate the largest solubilities, and Na has the highest (0.5%-1% in MgB7 at T=650-1000K ). All the considered interstitials have negligible solubilities. The solubility of Be in MgB7 cannot be determined because the corresponding low-solubility formation energy is negative indicating the existence of an unknown ternary ground state. We have performed a high-throughput search of ground states in binary Mg-B, Mg-A , and B-A systems, and we construct the ternary phase diagrams of Mg-B-A alloys based on the stable binary phases. Despite its high-temperature observations, we find that Sr9Mg38 is not a low-temperature equilibrium structure. We also determine two possible ground states CaB4 and RbB4 , not yet observed experimentally.

The capacity of hydrogen storage in alkali metal (Li, Na, or K), alkaline-earth metal (Be, Mg, or Ca), or Ti decorated borazine has been investigated by using the first-principles calculations based on density functional theory. Our results indicated that alkali metals could bind strongly to the inorganic molecule borazine and, especially, Li decorated borazine exhibits the highest hydrogen storage capacity up to 10.4 wt % theoretically. The adsorption energies of hydrogen molecules are in the range of -0.10˜-0.15 eV/H2 (-0.23˜-0.28 eV/H2 for local density approximation calculation) which are acceptable for reversible H2 adsorption/desorption near ambient temperature. We also found that the hydrogen storage capacity of Ti decorated borazine is about 7.2 wt %, less than that of the Li decorated system, but the adsorption energies are in the range of -0.16˜-0.24 eV/H2 due to the Kubas interaction, which is larger than that of the Li decorated borazine and the system is also suitable for reversible H2 adsorption/desorption near ambient temperature.

Firstprinciples calculations are performed to investigate the structural, electronic, elastic, and thermodynamic properties of the less known PrN compound for various space groups: NaCl(Fm3m(2 2 5)), CsCl(Pm3m (2 2 1)), ZB(F43m(2 1 6)), Wc(P6m2(1 8 7)), and CuAu (P4/mmm (1 2 3)). Our calculation indicates that the NaCl type structure is energetically more stable than the other phases. The calculated lattice parameters are consisted with available theoretical and experimental results. Our band structure calculations show that PrN possessess a semi-metallic character for both with and without spin polarized (SP) cases. The calculated elastic constants satisfy the mechanical stability conditions at all considered pressures and the present values are significantly higher than those of the previous results. The related mechanical properties such as Zener anisotropy factor ( A), Poisson’s ratio ( ?), Young’s modulus ( E), and shear modulus ( C) are also computed for NaCl structure. The temperature/pressure-dependent behaviours of bulk modulus, Debye temperature, heat capacity, thermal expansion coeffient, and V/ V0 ratio estimated within the quasi-harmonic Debye model.

CsMX3(M = Sn, Pb; X = Cl, Br, I) are strong candidates for the fast high energy irradiation detectors, ionic conductors, and optoelectronic devices. There are many experimental and theoretical investigations devoted to the study of perovskites ABX3 (A is a cation with different valence, B is a transition metal and X is oxides, halides or chlorides). But there is no systematic study of CsMX3 using HSE approximation particularly. In this paper, the band structures, density of states and optical properties of CsMX3(M = Sn, Pb; X = Cl, Br, I) have been studied by first-principles calculations using both the hybrid functional (HSE) approximation and the PBE-GGA approximation. The results of both approximations are compared with the experimental values. The results of HSE are closer to the experimental values. The changes of properties have been founded by comparing the band structures, density of states and optical properties of this series of thin film materials respectively. The trend of impact on these properties by replace elements has also been found. Our results provide a basis for the design of specific performance thin film materials.

We apply first-principles density-functional theory (DFT) calculations, ab-initio molecular dynamics, and the Kubo-Greenwood formula to predict electrical conductivity in Ta2Ox (0 ? x ? 5) as a function of composition, phase, and temperature, where additional focus is given to various oxidation states of the O monovacancy (VOn; n = 0,1+,2+). In the crystalline phase, our DFT calculations suggest that VO0 prefers equatorial O sites, while VO1+ and VO2+ are energetically preferred in the O cap sites of TaO7 polyhedra. Our calculations of DC conductivity at 300 K agree well with experimental measurements taken on Ta2Ox thin films (0.18 ? x ? 4.72) and bulk Ta2O5 powder-sintered pellets, although simulation accuracy can be improved for the most insulating, stoichiometric compositions. Our conductivity calculations and further interrogation of the O-deficient Ta2O5 electronic structure provide further theoretical basis to substantiate VO0 as a donor dopant in Ta2O5. Furthermore, this dopant-like behavior is specific to the neutral case and not observed in either the 1+ or 2+ oxidation states, which suggests that reduction and oxidation reactions may effectively act as donor activation and deactivation mechanisms, respectively, for VOn in Ta2O5.

Crystalline structures of magnesium hexaboride, MgB6, were investigated using unbiased structure searching methods combined with firstprinciples density functional calculations. An orthorhombic Cmcm structure was predicted as the thermodynamic ground state of MgB6. The energy of the Cmcm structure is significantly lower than the theoretical MgB6 models previously considered based on a primitive cubic arrangement of boron octahedra. The Cmcm structure is stable against the decomposition to elemental magnesium and boron solids at atmospheric pressure and high pressures up to 18.3 GPa. A unique feature of the predicted Cmcm structure is that the boron atoms are clustered into two forms: localized B6 octahedra and extended B? ribbons. Within the boron ribbons, the electrons are delocalized and this leads to a metallic ground state with vanished electric dipoles. The present prediction is in contrast to the previous proposal that the crystalline MgB6 maintains a semiconducting state with permanent dipole moments. MgB6 is estimated to have much weaker electron-phonon coupling compared with that of MgB2, and therefore it is not expected to be able to sustain superconductivity at high temperatures.

The search for technologically and economically viable storage solutions for hydrogen fuel would benefit greatly from research strategies that involve systematic property tuning of potential storage materials via atomic-level modification. Here, we use first-principles density-functional theory to investigate theoretically the structural and electronic properties of ultrathin Mg films and Mg-based alloy films and their interaction with atomic hydrogen. Additional delocalized charges are distributed over the Mg films upon alloying them with 11.1% of Al or Na atoms. These extra charges contribute to enhance the hydrogen binding strength to the films. We calculated the chemical potential of hydrogen in Mg films for different dopant species and film thickness, and we included the vibrational degrees of freedom. By comparing the chemical potential with that of free hydrogen gas at finite temperature (T) and pressure (P), we construct a hydrogenation phase diagram and identify the conditions for hydrogen absorption or desorption. The formation enthalpies of metal hydrides are greatly increased in thin films, and in stark contrast to its bulk phase, the hydride state can only be stabilized at high P and T (where the chemical potential of free H2 is very high). Metal doping increases the thermodynamic stabilities of the hydride films and thus significantly helps to reduce the required pressure condition for hydrogen absorption from H2 gas. In particular, with Na alloying, hydrogen can be absorbed and/or desorbed at experimentally accessible T and P conditions.

Reducing the amount of precious platinum (Pt) loading by identifying non-precious metal catalyst is essential for large-scale applications of fuel cells, which provide a cleaning energy technology. Recent experimental, theoretical, and simulation works accelerate the advance in the research area of doped carbon nanotubes acting as an alternate non-precious metal catalyst for dioxygen reduction in the fuel cells. Firstprinciples spin polarized density functional theory(DFT) simulations have been performed to understand O2 dissociation on nitrogen doped carbon nanotubes. We have studied nitrogen substitutional doping of carbon nanotubes (CNTs) for dioxygen adsorption, reduction, and dissociation. The calculated results show that nitrogen prefers to stay at the open-edge of short CNTs. Two O2 chemisorption sites are found, the carbon-nitrogen complex (Pauling site) and carbon-carbon long bridge (long bridge) sites. The spin polarized DFT calculations using the nudged elastic band (NEB) method show that O2 dissociation at the Pauling site has a reaction energy barrier of about 0.55 eV. The unique open-edge structure and charge redistribution are crucial to the novel properties of nitrogen-doped CNTs as a new non-precious metal catalyst for fuel cells.

First-principles calculations show that measured surface core-level shifts (SCLSs) of the GaAs(100)(2×4) surfaces can be described within the initial state effects. The calculated As3d and Ga3d SCLSs for the ?2 and ?2 reconstructions of the GaAs(100)(2×4) surfaces are in reasonable agreement with recent measurements. In particular, the results confirm that both the lower and the higher binding energy SCLSs, relative to the bulk emission in the As3d photoelectron spectra, are intrinsic properties of the GaAs(100)(2×4) surfaces. The most positive and most negative As shifts are attributed to the third layer As atoms, which differs from the previous intuitive suggestions. In general, calculations show that significant SCLSs arise from deep layers, and that there are more than two SCLSs. Our previously measured As3d spectra are fitted afresh using the calculated SCLSs. The intensity ratios of the SCLSs, obtained from the fits, show that as the heating temperature of the GaAs(100)(2×4) surface is increased gradually, the area of the ?2 reconstruction increases on the surface, but the ?2 phase remains within the whole temperature range, in agreement with previous experimental findings. Our results show that the combination of the experimental and theoretical results is a prerequisite for the accurate analysis of the SCLSs of the complex reconstructed surfaces.

Many inorganic pigments contain heavy metals hazardous to health and environment. Much attention has been devoted to the quest for nontoxic alternatives based on rare-earth elements. However, the computation of colors from firstprinciples is a challenge to electronic structure methods, especially for materials with localized f-orbitals. Here, starting from atomic positions only, we compute the colors of the red pigment cerium fluorosulfide as well as mercury sulfide (classic vermilion). Our methodology uses many-body theories to compute the optical absorption combined with an intermediate length-scale modelization to assess how coloration depends on film thickness, pigment concentration, and granularity. We introduce a quantitative criterion for the performance of a pigment. While for mercury sulfide, this criterion is satisfied because of large transition matrix elements between wide bands, cerium fluorosulfide presents an alternative paradigm: the bright red color is shown to stem from the combined effect of the quasi-2D and the localized nature of states. Our work shows the power of modern computational methods, with implications for the theoretical design of materials with specific optical properties. PMID:23302689

Many inorganic pigments contain heavy metals hazardous to health and environment. Much attention has been devoted to the quest for nontoxic alternatives based on rare-earth elements. However, the computation of colors from firstprinciples is a challenge to electronic structure methods, especially for materials with localized f-orbitals. Here, starting from atomic positions only, we compute the colors of the red pigment cerium fluorosulfide as well as mercury sulfide (classic vermilion). Our methodology uses many-body theories to compute the optical absorption combined with an intermediate length-scale modelization to assess how coloration depends on film thickness, pigment concentration, and granularity. We introduce a quantitative criterion for the performance of a pigment. While for mercury sulfide, this criterion is satisfied because of large transition matrix elements between wide bands, cerium fluorosulfide presents an alternative paradigm: the bright red color is shown to stem from the combined effect of the quasi-2D and the localized nature of states. Our work shows the power of modern computational methods, with implications for the theoretical design of materials with specific optical properties. PMID:23302689

Theoretical electronic structure techniques are used to analyze widely different systems from Si clusters to transition metal solids and surfaces. For the Si clusters, firstprinciples density functional methods are used to investigate Si{sub N} for N=2-8. Goal is to understand the different types of bonding that can occur in such small clusters where the atomic coordination differs substantially from tetrahedral bonding; such uncoordinated structures can test approximate models of Si surfaces. For the transition metal systems, non-self-consistent electronic structure methods are used to understand the driving force for surface relaxations. In-depth analysis of results is presented and physical basis of surface relaxation within the theory is discussed. Limitations inherent in calculations of metal surface relaxation are addressed. Finally, in an effort to understand approximate methods, a novel non-self- consistent density functional electronic structure method is developed that is about 1000 times faster than more sophisticated methods; this method is tested for various systems including diatomics, mixed clusters, surfaces, and bulk lattices.

The elastic properties, elastic anisotropy, and thermodynamic properties of the lately synthesized orthorhombic FeB4 at high pressures are investigated using first-principles density functional calculations. The calculated equilibrium parameters are in good agreement with the available experimental and theoretical data. The obtained normalized volume dependence of high pressure is consistent with the previous experimental data investigated using high-pressure synchrotron x-ray diffraction. The complete elastic tensors and crystal anisotropies of the FeB4 are also determined in the pressure range of 0-100 GPa. By the elastic stability criteria and vibrational frequencies, it is predicted that the orthorhombic FeB4 is stable up to 100 GPa. In addition, the calculated B/G ratio reveals that FeB4 possesses brittle nature in the range of pressure from 0 to 100 GPa. The calculated elastic anisotropic factors suggest that FeB4 is elastically anisotropic. By using quasi-harmonic Debye model, the compressibility, bulk modulus, the coefficient of thermal expansion, the heat capacity, and the Grüneisen parameter of FeB4 are successfully obtained in the present work.

In this contribution we investigate trends in the defect chemistry and hydration thermodynamics of rare-earth pyrochlore structured oxides, RE(2)X(2)O(7) (RE = La-Lu and X = Ti, Sn, Zr and Ce). Firstprinciples density functional theory (DFT) calculations have been performed to elucidate trends in the general defect chemistry and hydration enthalpy for the above-mentioned series. Further, to justify the use of such theoretical methods, the hydration properties of selected compositions were studied by means of thermogravimetric measurements. Both DFT calculations and TG measurements indicate that the hydration enthalpy becomes less exothermic with decreasing radii of RE ions within the RE(2)X(2)O(7) series (X = Ti, Sn, Zr and Ce), while it is less dependent on the X site ion. The observed hydration trends are discussed in connection with trends in the stability of both protons and oxygen vacancies and changes in the electronic density of states and bonding environment through the series. Finally, the findings are discussed with respect to existing correlations for other binary and ternary oxides. PMID:23001186

The structural, electronic, and transport properties of AgSbTe2 are studied by using full-relativistic first-principles electronic structure calculation and semiclassical description of transport parameters. The results indicate that, within various exchange-correlation functionals, the cubic F d 3 ¯ m and trigonal R 3 ¯ m structures of AgSbTe2 are more stable than two other considered structures. The computed Seebeck coefficients at different values of the band gap and carrier concentration are accurately compared with the available experimental data to speculate a band gap of about 0.1-0.35 eV for AgSbTe2 compound, in agreement with our calculated electronic structure within the hybrid HSE (Heyd-Scuseria-Ernzerhof) functional. By calculating the semiclassical Seebeck coefficient, electrical conductivity, and electronic part of thermal conductivity, we present the theoretical upper limit of the thermoelectric figure of merit of AgSbTe2 as a function of temperature and carrier concentration.

The structures, energetics, vertical and adiabatic ionization potentials, electron affinities, and global reactivity descriptors of antioxidant vitamins (both water- and fat-soluble) in neutral, positively charged, and negatively charged states were investigated theoretically. We worked within the framework of first-principles density functional theory (DFT), using the B3LYP functional and both localized (6-311G+(d,p) and plane-wave basis sets. Solvent effects were modeled via the polarizable continuum model (PCM), using the integral equation formalism variant (IEFPCM). From the computed structural parameters, ionization potentials, electron affinities, and spin densities, we deduced that these vitamins prefer to lose electrons to neutral reactive oxygen species (·OH and ·OOH), making them good antioxidants. Conceptual DFT was used to determine global chemical reactivity parameters. The computed chemical hardnesses showed that these antioxidant vitamins are more reactive than neutral reactive oxygen species (ROS), thus supporting their antioxidant character towards these species. However, in the neutral state, these vitamins do not act as antioxidants for [Formula: see text]. The reactivity of vitamins towards ROS depends on the nature of the solvent. Amongst the ROS, ·OH has the greatest propensity to attract electrons from a generic donor. The reactivities of fat-soluble vitamins towards neutral reactive oxygen species were found to be larger than those of water-soluble vitamins towards these species, showing that the former are better antioxidants. PMID:23625032

We report first-principlestheoretical investigations of possible metal contacts to monolayer black phosphorus (BP). By analyzing lattice geometry, five metal surfaces are found to have minimal lattice mismatch with BP: Cu(111), Zn(0001), In(110), Ta(110), and Nb(110). Further studies indicate Ta and Nb bond strongly with monolayer BP causing substantial bond distortions, but the combined Ta-BP and Nb-BP form good metal surfaces to contact a second layer BP. By analyzing the geometry, bonding, electronic structure, charge transfer, potential, and band bending, it is concluded that Cu(111) is the best candidate to form excellent Ohmic contact to monolayer BP. The other four metal surfaces or combined surfaces also provide viable structures to form metal/BP contacts, but they have Schottky character. Finally, the band bending property in the current-in-plane (CIP) structure where metal/BP is connected to a freestanding monolayer BP, is investigated. By both work function estimates and direct calculations of the two-probe CIP structure, we find that the freestanding BP channel is n type.

The structure and mechanical properties of tantalum mononitride (TaN) are investigated at high pressure from first-principles using the plane wave pseudopotential method within the local density approximation. Three stable phases were considered, i.e., two hexagonal phases (? and ?) and a cubic ? phase. The obtained equilibrium structure parameters and ground state mechanical properties are in excellent agreement with the experimental and other theoretical results. A full elastic tensor and crystal anisotropy of the ultra-incompressible TaN in three stable phases are determined in the wide pressure range. Results indicated that the elastic properties of TaN in three phases are strongly pressure dependent. And the hexagonal ?-TaN is the most ultraincompressible among the consider phases, which suggests that the ? phase of TaN is a potential candidate structure to be one of the ultraincompressible and hard materials. By the elastic stability criteria, it is predicted that ?-TaN is not stable above 53.9 GPa. In addition, the calculated B/G ratio indicated that the ? and ? phases possess brittle nature in the range of pressure from 0 to 100?GPa. While ? phase is brittleness at low pressure (below 8.2?GPa) and is strongly prone to ductility at high pressure (above 8.2?GPa). The calculated elastic anisotropic factors for three phases of TaN suggest that they are elastically highly anisotropic and strongly dependent on the propagation direction. PMID:23185097

?-Fe2O3 (Hematite) is of special interest in the design of multifunctional structural energetic materials (SEM), based on a thermite mixture of metal and metal oxide. In this paper, from first-principles, we obtained the thermodynamically complete EOS P = P(?,T) for hematite for pressures up to 50GPa and temperatures up to 1000K. There are only a few theoretical works on hematite. The difficulty of techniques traces back to the complication of the description of highly correlated d-electrons induced localization of valence states in Fe, and the mixing of the O 2p states and the Fe 3d states. In this paper, we implemented the ground state calculations in the framework of DFT, using sGGA and projector augmented wave approach. Particularly, the Hubbard-U method is used to describe the on-site Coulomb interactions of strongly correlated d-electrons in Fe atoms. The lattice thermal contributions are obtained by populating the phonon modes, according to the Boltzmann statistics. In comparison to the previous studies, the thermal contributions to EOS from lattice vibrations are included. In addition, we investigate the magnetic phase transitions at pressures and temperatures of interest. In the applications of SEMs, pressures are lower than 50 GPa which exclude the HP phases. The phonon dispersion curves with Hubbard-U are compared with those without Hubbard-U.

The proper description of the electric environment of condensed phases is a critical challenge for force field methods. To test and validate the ability of the CHARMM additive force field to describe the electric environment in aqueous solution combined QM/MM calculations have been used to calculate the vibrational Stark effect (VSE). We utilized a firstprinciples methodology using correlated electronic structure techniques to compute the Stark shift between the gas phase and solvent environments and between two different solvent environments of three VSE probes containing acetonitrile or fluorine functionalities which have been well-characterized experimentally. Reasonable agreement with the experimentally determined Stark shifts is obtained when the MM atoms are described by the CHARMM additive force field, though it is essential to employ an anharmonic correction in the frequency calculation. In addition, the electric field created by the solvent is computed along the CN bond and a theoretical Stark tuning rate is determined for acetonitrile and shown to be in satisfactory agreement with experiment. PMID:21423871

An oP10-FeB4 phase [H. Gou, et al., Phys. Rev. Lett., 2013, 111, 157002] was recently synthesized based on previous theoretical predictions. In this study, a high-pressure phase of FeB4 (tP10-FeB4) was proposed through first-principles calculations. The tP10-FeB4 structure, which contains two formula units per unit cell, belongs to tetragonal symmetry with the space group P42/nmc. The boron atoms in tP10-FeB4 are present as tetrahedron configurations. Enthalpies as a function of pressure indicate that this new phase is probable to achieve through a phase transition from the oP10-FeB4 phase above ?65.9 GPa. The softening of acoustic phonon at T points in the Brillouin zone may be the driving force behind the phase transition. Further analyses reveal that the tP10-FeB4 phase is a potential superhard semiconductor. PMID:25204967

Dye-sensitized quantum dots (QDs) are considered promising candidates for dye-sensitized solar cells. In order to maximize their efficiency, detailed theoretical studies are important. Here, we report a firstprinciples density functional theory (DFT) investigation of experimentally realized dye - sensitized QD / ligand systems, viz., Cd16S16, capped with acetate molecules and a coumarin dye. The hybrid B3LYP functional and a 6-311+G(d,p)/LANL2dz basis set are used to study the geometric, energetic and electronic properties of these clusters. There is significant structural rearrangement in all the clusters studied - on the surface for the bare QD, and in the positions of the acetate / dye ligands for the ligated QDs. The density of states (DOS) of the bare QD shows states in the band gap, which disappear on surface passivation with the acetate molecules. Interestingly, in the dye-sensitised QD, the HOMO is found to be localized mainly on the dye molecule, while the LUMO is on the QD, as required for photo-induced electron injection from the dye to the QD.

We have studied the nuclear quadrupole interactions (NQI) of the 14N, 17O and 2H nuclei in the nucleobases cytosine, adenine, guanine and thymine in the free state as well as when they are bonded to the sugar ring in DNA, simulated through a CH3 group attached to the nucleobases. The nucleobase uracil, which replaces thymine in RNA, has also been studied. Our results show that there are substantial indirect effects of the bonding with the sugar group in the nucleic acids on the NQI parameters e 2 qQ/h and ?. It is hoped that measurements of these NQI parameters in DNA will be available in the future to compare with our predictions. Our results provide the conclusion that for any property dependent on the electronic structures of the nucleic acids, the effects of the bonding between the nucleobases and the nucleic acid backbones have to be included.

We have studied the nuclear quadrupole interactions (NQI) of the 14N, 17O and 2H nuclei in the nucleobases cytosine, adenine, guanine and thymine in the free state as well as when they are bonded to the sugar ring in DNA, simulated through a CH3 group attached to the nucleobases. The nucleobase uracil, which replaces thymine in RNA, has also been studied. Our results show that there are substantial indirect effects of the bonding with the sugar group in the nucleic acids on the NQI parameters e 2 qQ/h and ?. It is hoped that measurements of these NQI parameters in DNA will be available in the future to compare with our predictions. Our results provide the conclusion that for any property dependent on the electronic structures of the nucleic acids, the effects of the bonding between the nucleobases and the nucleic acid backbones have to be included.

We present an extensive study of the stationary points on the acetylene-water (AW) ground-state potential energy surface (PES) aimed in establishing accurate energetics for the two different bonding scenarios that are considered. Those include arrangements in which water acts either as a proton acceptor from one of the acetylene hydrogen atoms or a proton donor to the triple bond. We used a hierarchy of theoretical methods to account for electron correlation [MP2 (second-order Moller-Plesset), MP4 (fourth-order Moller-Plesset), and CCSD(T) (coupled-cluster single double triple)] coupled with a series of increasing size augmented correlation consistent basis sets (aug-cc-pVnZ, n=2,3,4). We furthermore examined the effect of corrections due to basis set superposition error (BSSE). We found that those have a large effect in altering the qualitative features of the PES of the complex. They are responsible for producing a structure of higher (C{sub 2v}) symmetry for the global minimum. Zero-point energy (ZPE) corrections were found to increase the stability of the C{sub 2v} arrangement. For the global (water acceptor) minimum of C{sub 2v} symmetry our best estimates are {delta}E{sub e}=-2.87 kcal/mol ({delta}E{sub 0}=-2.04 kcal/mol) and a van der Waals distance of R{sub e}=2.190 Aa. The water donor arrangement lies 0.3 kcal/mol (0.5 kcal/mol including ZPE corrections) above the global minimum. The barrier for its isomerization to the global minimum is E{sub e}=0.18 kcal/mol; however, inclusion of BSSE- and ZPE-corrections destabilize the water donor arrangement suggesting that it can readily convert to the global minimum. We therefore conclude that there exists only one minimum on the PES in accordance with previous experimental observations. To this end, vibrational averaging and to a lesser extend proper description of intermolecular interactions (BSSE) were found to have a large effect in altering the qualitative features of the ground-state PES of the acetylene-water complex. (c) 2000 American Institute of Physics.

This thesis presents an ab initio study of biological molecules using first-principles molecular dynamics. Density functional theory and Car-Parrinello molecular dynamics are used in the computational modeling of the water ...

First-principles atomistic simulation is a vital tool for understanding the properties of materials at the high-pressure high-temperature conditions prevalent in giant planet interiors, but properties such as solubility and phase boundaries are dependent on entropy, a quantity not directly accessible in simulation. Determining entropic properties from atomistic simulations is a difficult problem typically requiring a time-consuming integration over molecular dynamics trajectories. Here I will describe recent advances in first-principles thermodynamic calculations which substantially increase the simplicity and efficiency of thermodynamic integration and make entropic properties more readily accessible. I will also describe the use of first-principles thermodynamic calculations for understanding problems including core solubility in gas giants and superionic phase changes in ice giants, as well as future prospects for combining first-principles thermodynamics with planetary-scale models to help us understand the origin and consequences of compositional inhomogeneity in giant planet interiors.

In this thesis, we show for the first time how it is possible to calculated fully from first-principles the diabatic free-energy surfaces of electron-transfer reactions. The excitation energy corresponding to the transfer ...

In this paper, thermal conductivity of crystalline GaAs is calculated using first-principles lattice dynamics. The harmonic and cubic force constants are obtained by fitting them to the force-displacement data from density ...

The idea of first-principles methods is to determine the properties of materials by solving the basic equations of quantum mechanics and statistical mechanics. With such an approach, one can, in principle, predict the ...

The ability to predict a semiconductor's band edge positions in solution is important for the design of water-splitting photocatalyst materials. In this paper, we introduce a first-principles method to compute the ...

A first-principles model of the electrochemical double layer is applied to study surface energies and surface coverage under realistic electrochemical conditions and to determine the equilibrium shape of metal nanoparticles ...

The structural properties of graphene/Ni(111) are investigated by a combination of low-energy electron diffraction (LEED), x-ray photoelectron spectroscopy (XPS), angle-scanned photoelectron diffraction (PED), and first-principles calculations. XPS data indicate that graphene interacts strongly with the topmost Ni layer. Diffraction data show that graphene is deposited commensurably with the underlying Ni surface atoms. Twelve different graphene preparations were analyzed by LEED and one by PED. Considering the relative position between the carbon and Ni atoms, five experimental sets indicate a top-fcc structure, three show a bridge-top structure, and four have a mixed structure. The analysis of the PED experiment suggests the top-fcc termination. Our first-principles calculations show that the total energies of the top-fcc and bridge-top structures are nearly degenerate, which corroborates the observed bistability of those phases. Moreover, by comparing the structural parameters obtained by the three methods (LEED, PED, and ab initio calculations), excellent agreement is achieved.

The conclusions of the application of firstprinciples model to spacecraft operations are: the firstprinciples of Bi-phasic electrode presented model provides an explanation for many behaviors on voltage fading on LEO cycling.

Spinel phase aluminum oxynitride solid solution (?-alon, with formula of Al(8+x)/3O4-xNx) exists in the narrow Al2O3-rich region of Al2O3-AlN systems. The first-principles calculations were developed to investigate the composition-dependent bonding and hardness of ?-alon. Six supercell model for Al(8+x)/3O4-xNx (x = 0, 0.25, 0.44, 0.63, 0.81, and 1) was constructed to perform our calculations with high accuracy. It was found that the lattice constant increases with increasing composition of nitrogen in ?-alon. The bond lengths of AlIV-O, AlVI-O, AlIV-N, and AlVI-N all increase with the expansion of crystal structure. The well-known Mulliken overlap populations were calculated to estimate the bonding and hardness. As the content of nitrogen substitute increases, the Al-N bonds present more covalent characteristic, while the Al-O bonds present more ionic characteristic. The AlIV-N is the hardest bond in ?-alon. The theoretical hardness of ?-alon could be slightly enhanced from 17.16 GPa to 17.97 GPa by increasing content of nitrogen in full solubility range. The contribution ratio, CH?, was proposed to quantify the contribution of bonds to hardness of ?-alon. The Al-O bonds are found to contribute more to the hardness. The Al-N bonds are the main influencing factor to enhance the hardness of ?-alon. These calculated results provide the basis for understanding the composition-dependent bonding and hardness of ?-alon.

Socio-ecological dynamics emerged from the field of Mathematical SocialSciences and opened up avenues for re-examination of classical problems of collective behavior in Social and Spatial sciences. The ``engine" of this collective behavior is the subjective mental evaluation of level of utilities in the future, presenting sets of composite socio-economic-temporal-locational advantages. These dynamics present new laws of collective multi-population behavior which are the meso-level counterparts of the utility optimization individual behavior. The central core of the socio-ecological choice dynamics includes the following firstprinciple of the collective choice behavior of ``Homo Socialis" based on the existence of ``collective consciousness": the choice behavior of ``Homo Socialis" is a collective meso-level choice behavior such that the relative changes in choice frequencies depend on the distribution of innovation alternatives between adopters of innovations. The mathematical basis of the Socio-Ecological Dynamics includes two complementary analytical approaches both based on the use of computer modeling as a theoretical and simulation tool. First approach is the ``continuous approach" --- the systems of ordinary and partial differential equations reflecting the continuous time Volterra ecological formalism in a form of antagonistic and/or cooperative collective hyper-games between different sub-sets of choice alternatives. Second approach is the ``discrete approach" --- systems of difference equations presenting a new branch of the non-linear discrete dynamics --- the Discrete Relative m-population/n-innovations Socio-Spatial Dynamics (Dendrinos and Sonis, 1990). The generalization of the Volterra formalism leads further to the meso-level variational principle of collective choice behavior determining the balance between the resulting cumulative social spatio-temporal interactions among the population of adopters susceptible to the choice alternatives and the cumulative equalization of the power of elites supporting different choice alternatives. This balance governs the dynamic innovation choice process and constitutes the dynamic meso-level counterpart of the micro-economic individual utility maximization principle.

We apply first-principles density-functional theory (DFT) calculations, ab-initio molecular dynamics, and the Kubo-Greenwood formula to predict electrical conductivity in Ta{sub 2}O{sub x} (0???x???5) as a function of composition, phase, and temperature, where additional focus is given to various oxidation states of the O monovacancy (V{sub O}{sup n}; n?=?0,1+,2+). In the crystalline phase, our DFT calculations suggest that V{sub O}{sup 0} prefers equatorial O sites, while V{sub O}{sup 1+} and V{sub O}{sup 2+} are energetically preferred in the O cap sites of TaO{sub 7} polyhedra. Our calculations of DC conductivity at 300?K agree well with experimental measurements taken on Ta{sub 2}O{sub x} thin films (0.18???x???4.72) and bulk Ta{sub 2}O{sub 5} powder-sintered pellets, although simulation accuracy can be improved for the most insulating, stoichiometric compositions. Our conductivity calculations and further interrogation of the O-deficient Ta{sub 2}O{sub 5} electronic structure provide further theoretical basis to substantiate V{sub O}{sup 0} as a donor dopant in Ta{sub 2}O{sub 5}. Furthermore, this dopant-like behavior is specific to the neutral case and not observed in either the 1+ or 2+ oxidation states, which suggests that reduction and oxidation reactions may effectively act as donor activation and deactivation mechanisms, respectively, for V{sub O}{sup n} in Ta{sub 2}O{sub 5}.

The structural determination, thermodynamic, mechanical, dynamic and electronic properties of 4d transitional metal diborides MB2 (M = Y-Ag) are systematically investigated by first-principles within the density functional theory (DFT). For each diboride, five structures are considered, i.e. AlB2-, ReB2-, OsB2-, MoB2- and WB2-type structures. The calculated lattice parameters are in good agreement with the previously theoretical and experimental studies. The formation enthalpy increases from YB2 to AgB2 in AlB2-type structure (similar to MoB2- and WB2-type). While the formation enthalpy decreases from YB2 to MoB2, reached minimum value to TcB2, and then increases gradually in ReB2-type structure (similar to OsB2-type), which is consistent with the results of the calculated density of states. The structural stability of these materials relates mainly on electronegative of metals, boron structure and bond characters. Among the considered structures, TcB2-ReB2 (TcB2-ReB2 represents TcB2 in ReB2-type structure, the same hereinafter) has the largest shear modulus (248 GPa), and is the hardest compound. The number of electrons transferred from metals to boron atoms and the calculated densities of states (DOS) indicate that each diboride is a complex mixture of metallic, ionic and covalent characteristics. Trends are discussed.

A recent experiment [H. Y. Gou et al., Phys. Rev. Lett. 111, 157002 (2013), 10.1103/PhysRevLett.111.157002] reported a measured Vickers hardness of over 60 GPa for FeB4, placing it as a superhard material far above all other similar ultrahard transition-metal borides, such as ReB2,WB4, and especially CrB4, which has the same crystalline structure as that of FeB4 but a much lower measured Vickers hardness of around 23 GPa. This result, however, is contradicted by theoretical calculations that predict a smaller shear modulus for FeB4 than that of CrB4, indicating that FeB4 is softer than CrB4. Here we report first-principles calculations that aim to understand the stress response of FeB4 under indentation loadings and examine whether there exists a strain-stiffening effect that might enhance the indentation strength. Our results show that there is no strain stiffening in FeB4; instead, the normal pressure beneath the indenter drives a lateral structural expansion which further stretches and weakens the boron-boron and boron-iron bonds in addition to that caused by the shear deformation in Vickers indentation tests. This effect leads to a considerably reduced strength of FeB4, producing an ideal (i.e., an upper bound) indentation strength of 17 GPa that is lower than that (27 GPa) predicted for CrB4. The present results suggest that FeB4 is unlikely to be superhard and further experimental investigation is needed to clarify this issue.

The edge reconstructions of hexagonal boron nitride nanoribbons (BNNRs) and their stabilities have been investigated by the first-principles calculations of both their binding and edge energies. It is found from our calculations that the binding energy we have used is a reliable and useful quantity for judging the stabilities of different edge reconstructions of the hetero-elemental BNNRs instead of the conventional edge energy one, especially for those BNNR's edges with unequal number of B and N atoms. In addition, other four main results have been obtained: (1) the armchair BNNR is the most stable edge structure and the characteristic ac-48 edge reconstruction for the BNNRs is predicted to be the second most stable edge in all the discussed BNNR edge structures. But, its zigzag edge is less stable. (2) The zigzag-like ac-56 type reconstructions are more stable than the pristine zigzag structures, which is different from that of the graphene nanoribbon (GNR), being less stable than the zigzag GNR. (3) The stabilities of BNNR's ac-677 and ac-678 type edge reconstructions lie between its ac-56-B and zz-57-B edges. (4) The zz-57-B(-N) edge reconstruction lowers the edge energy by a small quantity, which is also different from that of GNR. Moreover, the zz-57-B edge structure is more stable than the zz-57-N one, indicating that B-rich edge is easier to be reconstructed while the N-rich edge is more stable. Our theoretical calculations suggest the many possible reconstructed edge structures for the bare BNNRs, which is important for BNNR's application in future nanoelectronics and spintronics.

Using the nonequilibrium Green's function (NEGF) formalism, we derive the current density formula for ac quantum transport by including the self-consistent Coulomb interaction. It is well known that the Coulomb interaction is very important in determining ac current in nanostructures. As pointed out by Büttiker that the Coulomb interaction must be included to conserve the ac current. Theoretically, the displacement current can be accounted for by including a self-consistent Hartree term in the Hamiltonian as well as the exchange and correlation term while the ac current is calculated from particle current, i.e., =q where N?? is the number operator of the ? lead. For the ac current density, however, the Coulomb interaction contributes in two ways. As the case of ac current, the self-consistent Coulomb interaction has to be included in the conventional particle current density. In addition, we have to consider the displacement current density explicitly, which is proportional to the time derivative of displacement field. Once the ac current density is obtained, one can calculate the ac current by integrating it over a cross-section area along the transport direction. It is shown that ac current obtained from the total ac current density is conserved and equal to that calculated directly from the lead using NEGF theory. We have applied our formalism to calculate ac current density for nanodevices by combining the density functional theory (DFT) with NEGF theory. Specifically, we have calculated the ac current density to the first order of frequency in a molecular device Al-C4-Al from firstprinciples. It is found that Al-C4-Al system exhibits inductive-like behavior under ac bias in the low-frequency limit. Furthermore, nonequilibrium charge distribution is obtained that enables us to study electrochemical capacitance of the molecular devices.

In this study we focus on the differences and analogies of two experimental implementations of two-dimensional infrared (2D-IR) spectroscopy: double-resonance or dynamic hole burning 2D-IR spectroscopy and pulsed Fourier transform or heterodyne detected photon echo spectroscopy. A comparison is done theoretically as well as experimentally by contrasting data obtained from both methods. As an example we have studied the strongly

Size-selected Wn clusters can be deposited firmly on a graphite (0001) surface using a novel technique, where the positive ions (of the same metal atom species) embedded on the graphite surface by ion implantation, act as anchors. The size selected metal clusters can then soft land on this anchored surface m [Hayakawa et al., 2009]. We have carried out a systematic theoretical study of the adsorption of Wn (n = 1-6) clusters on anchored graphite (0001) surface, using state-of-art spin-polarized density functional approach. In our first-principles calculations, the graphite (0001) surface has been suitably modeled as a slab separated by large vacuum layers. Wn clusters bond on clean graphite (0001) surface with a rather weak Van-der-Waals interaction. However, on the anchored graphite (0001) surface, the Wn clusters get absorbed at the defect site with a much larger adsorption energy. We report here the results of our first-principles investigation of this supported Wn cluster system, along with their reactivity trend as a function of the cluster size (n).

A symbolic programming package N Coperators with applications to atomic physics is introduced. The package runs over Mathematica and it implements NC Algebra, the noncommutative algebra package. N Coperators features the algebra of irreducible tensor operators, the second quantization representation, the angular momentum theory, and the effective operator approach exploited in many-body perturbation theory, including Wick's theorem. The comprehensiveness is yet another characteristic feature of the present package: The generation of expressions is performed in a way as if it were done by hand. Although the theoretical atomic spectroscopy is a direct target of N Coperators, the package, with minor modifications, if any, is believed to appropriate other areas of theoretical physics as well.

Recently, the quaternary compounds, Cu2ZnSnS4 and Cu2ZnSnSe4, have been attracted pretty much attention because of their potential use in the field of energy harvesting applications. Several theoretical calculations have been reported about their firstprinciples electronic, optic and transport properties. However, no lattice dynamic calculations have been published yet despite the discussions about their possible ground state crystal structures and

In the course of my PhD I have worked on a broad range of problems using simulations from firstprinciples: from catalysis and chemical reactions at surfaces and on nanostructures, characterization of carbon-based systems and devices, and surface and interface physics. My research activities focused on the application of ab-initio electronic structure techniques to the theoretical study of important aspects of the physics and chemistry of materials for energy and environmental applications and nano-electronic devices. A common theme of my research is the computational study of chemical reactions of environmentally important molecules (CO, CO2) using high performance simulations. In particular, my principal aim was to design novel nano-structured functional catalytic surfaces and interfaces for environmentally relevant remediation and recycling reactions, with particular attention to the management of carbon dioxide. We have studied the carbon-mediated partial sequestration and selective oxidation of carbon monoxide (CO), both in the presence and absence of hydrogen, on graphitic edges. Using first-principles calculations we have studied several reactions of CO with carbon nanostructures, where the active sites can be regenerated by the deposition of carbon decomposed from the reactant (CO) to make the reactions self-sustained. Using statistical mechanics, we have also studied the conditions under which the conversion of CO to graphene and carbon dioxide is thermodynamically favorable, both in the presence and in the absence of hydrogen. These results are a first step toward the development of processes for the carbon-mediated partial sequestration and selective oxidation of CO in a hydrogen atmosphere. We have elucidated the atomic scale mechanisms of activation and reduction of carbon dioxide on specifically designed catalytic surfaces via the rational manipulation of the surface properties that can be achieved by combining transition metal thin films on oxide substrates. We have analyzed the mechanisms of the molecular reactions on the class of catalytic surfaces so designed in an effort to optimize materials parameters in the search of optimal catalytic materials. All these studies are likely to bring new perspectives and substantial advancement in the field of high-performance simulations in catalysis and the characterization of nanostructures for energy and environmental applications. Moving to novel materials for electronics applications, I have studied the structural and vibrational properties of mono and bi-layer graphene. I have characterized the lattice thermal conductivity of ideal monolayer and bi-layer graphene, demonstrating that their behavior is similar to that observed in graphite and indicating that the intra-layer coupling does not affect significantly the thermal conductance. I have also calculated the electron-phonon interaction in monolayer graphene and obtained electron scattering rates associated with all phonon modes and the intrinsic resistivity/mobility of monolayer graphene is estimated as a function of temperature. On another project, I have worked on ab initio molecular dynamic studies of novel Phase Change Materials (PCM) for memory and 3D-integration. We characterized high-temperature, sodium | nickel chloride, rechargeable batteries. These batteries are under consideration for hybrid drive systems in transportation applications. As part of our activities to improve performance and reliability of these batteries, we developed an engineering transport model of the component electrochemical cell. To support that model, we have proposed a reaction kinetics expression for the REDOX (reduction-oxidation) reaction at the porous positive electrode. We validate the kinetics expression with electrochemical measurements. A methodology based on the transistor body effect is used to estimate inversion oxide thicknesses (Tinv) in high-kappa/metal gate, undoped, ultra-thin body SOI FINFETs. The extracted Tinvs are compared to independent capacitance voltage (CV) measurements.

To optimally design next generation catalysts a thorough understanding of the chemical phenomena at the molecular scale is a prerequisite. Apart from qualitative knowledge on the reaction mechanism, it is also essential to be able to predict accurate rate constants. Molecular modeling has become a ubiquitous tool within the field of heterogeneous catalysis. Herein, we review current computational procedures to determine chemical kinetics from firstprinciples, thus by using no experimental input and by modeling the catalyst and reacting species at the molecular level. Therefore, we use the methanol-to-olefin (MTO) process as a case study to illustrate the various theoretical concepts. This process is a showcase example where rational design of the catalyst was for a long time performed on the basis of trial and error, due to insufficient knowledge of the mechanism. For theoreticians the MTO process is particularly challenging as the catalyst has an inherent supramolecular nature, for which not only the Brønsted acidic site is important but also organic species, trapped in the zeolite pores, must be essentially present during active catalyst operation. All these aspects give rise to specific challenges for theoretical modeling. It is shown that present computational techniques have matured to a level where accurate enthalpy barriers and rate constants can be predicted for reactions occurring at a single active site. The comparison with experimental data such as apparent kinetic data for well-defined elementary reactions has become feasible as current computational techniques also allow predicting adsorption enthalpies with reasonable accuracy. Real catalysts are truly heterogeneous in a space- and time-like manner. Future theory developments should focus on extending our view towards phenomena occurring at longer length and time scales and integrating information from various scales towards a unified understanding of the catalyst. Within this respect molecular dynamics methods complemented with additional techniques to simulate rare events are now gradually making their entrance within zeolite catalysis. Recent applications have already given a flavor of the benefit of such techniques to simulate chemical reactions in complex molecular environments. PMID:25054453

Computer simulation plays a critical role in connecting microscopic structure and macroscopic mechanical properties of structural material, which is a key factor that needs to be considered in design of such kind of material. Via the quantum mechanics first-principles calculations, one can gain structure, elastic constant, energetics, and stress of selected material system, based on which one is able to predict the mechanical properties or provide useful insights for the mechanical properties of the materials. This can be done either directly or in combination with the empirical criterions. This paper reviews the recent research advances on the attempts to predict the mechanical properties of structural materials from firstprinciples.

We investigated the dynamics of zinc (Zn) and oxygen (O) adsorbed atoms (adatoms) on a Zn-polar ZnO(0001) surface using the first-principles calculation. The results of the first-principles calculation revealed that a high-quality ZnO crystalline growth condition is induced by wurtzite structure packing under a Zn-rich growth condition using a Zn-polar ZnO(0001) surface. However, it was shown that an O adatom is not sufficient to promote surface atomic diffusion. For high-quality ZnO crystal, promoting surface diffusion of adatoms using high temperature is important.

The high-pressure behaviors of crystalline BeF2 are investigated theoretically by using first-principles plane-wave pseudopotential density functional theory within the local density approximation (LDA). The results demonstrate that the sequence of the pressure-induced phase transitions of BeF2 under 50 GPa is from the ?-quartz-type, to coesite-type, rutile-type, and ?-PbO2-type structures. Moreover, the electronic properties of BeF2 with different crystal structures are analyzed. The results show that the electronic structures of BeF2 are fairly insensitive to the particular crystal structures, which are determined mainly by the BeF4 tetrahedron (or BeF6 octahedra). At last, the effects of pressure on the electronic structures of BeF2 are discussed. The band gap of BeF2 is found to become broader with increase of pressure.

The phase transition kinetics of HgS from cinnabar to rocksalt structure under high pressure was studied by first-principle computations. The calculations have been performed using the density functional theory (DFT) and the augmented plane wave (APW) plus local orbitals (LO) basis set. The calculations clarify the argument about the phase transition pressure and verify it is a second-order phase transition theoretically. The results also describe the variations of parameters a , c , c/a and the atom fractional coordinates u and v during the phase-transition process. The simulation of the atomic configurations under different pressures depicts the phase-transition process as two steps, i.e., the relaxation and reconstruction of the Hg?S helical chains.

We have performed first-principles density functional theory calculations to investigate the possible physical origins of the discrepancies between the existing theoretical and experimental studies on cation distribution in MgX2O4 (X = Al, Ga, In) spinel oxides. We show that for MgGa2O4 and MgIn2O4, it is crucial to consider the effects of lattice vibrations to achieve agreement between theory and experiment. For MgAl2O4, we find that neglecting short-range order effects in thermodynamic modeling can lead to significant underestimation of the degree of inversion. Furthermore, we demonstrate that the common practice of representing disordered structures by randomly exchanging atoms within a small periodic supercell can incur large computational error due to either insufficient statistical sampling or finite supercell size effects.

The magnetization behaviour of the ferromagnetic shape memory Heusler Ni2MnGa alloy under applied magnetic fields is studied using first-principles and Monte Carlo (MC) calculations. Calculations were carried out for single-crystal and polycrystalline structures with magnetic domains. In the multi-domain approach, the stochastic competition between the magnetic anisotropy field and the external magnetic field is taken into account by introducing a probability factor. By constructing a complex Hamiltonian model with ab initio input parameters, we can predict the temperature dependence of the magnetization in Heusler alloys for low and high magnetic fields by means of MC simulations. The theoretical iso-field magnetization curves are in good agreement with experimental data.

Using first-principles calculations, the structural and elastic properties of Sc 2AC, with A=Al, Ga, In and Tl, were studied by means of the pseudo-potential plane-waves method. Calculations were performed within the local density approximation to the exchange-correlation approximation energy. The effect of high pressures, up to 20 GPa, on the lattice constants and the internal parameters is calculated. The elastic constants are calculated using the static finite strain technique. We derived the bulk and shear moduli, Young's moduli and Poisson's ratio for ideal polycrystalline Sc 2AC aggregates. We estimated the Debye temperature of Sc 2AC from the average sound velocity. This is the first quantitative theoretical prediction of the elastic properties of Sc 2AlC, Sc 2GaC, Sc 2InC and Sc 2TlC compounds, and it still awaits the experimental confirmation.

Knowledge of near infrared intensities of rovibrational transitions of polyatomic molecules is essential for the modeling of various planetary atmospheres, brown dwarfs and for other astrophysical applications 1,2,3. For example, to analyze exoplanets, atmospheric models have been developed, thus making the need to provide accurate spectroscopic data. Consequently, the spectral characterization of such planetary objects relies on the necessity of having adequate and reliable molecular data in extreme conditions (temperature, optical path length, pressure). On the other hand, in the modeling of astrophysical opacities, millions of lines are generally involved and the line-by-line extraction is clearly not feasible in laboratory measurements. It is thus suggested that this large amount of data could be interpreted only by reliable theoretical predictions. There exists essentially two theoretical approaches for the computation and prediction of spectra. The first one is based on empirically-fitted effective spectroscopic models. Another way for computing energies, line positions and intensities is based on global variational calculations using ab initio surfaces. They do not yet reach the spectroscopic accuracy stricto sensu but implicitly account for all intramolecular interactions including resonance couplings in a wide spectral range. The final aim of this work is to provide reliable predictions which could be quantitatively accurate with respect to the precision of available observations and as complete as possible. All this thus requires extensive first-principles quantum mechanical calculations essentially based on three necessary ingredients which are (i) accurate intramolecular potential energy surface and dipole moment surface components well-defined in a large range of vibrational displacements and (ii) efficient computational methods combined with suitable choices of coordinates to account for molecular symmetry properties and to achieve a good numerical convergence. Because high-resolution ab initio spectra predictions for systems with N>4 atoms is a very challenging task, the major issue is to minimize the cost of computations and the loss of accuracy during calculations. To this end, a truncation-reduction technique for the Hamiltonian operator as well as an extraction-compression procedure for the basis set functions will be introduced and discussed in detail. We will give a review on the recent progress in computational methods as well as on existing experimental and theoretical databases 4,5,6,7,8,9. This presentation will be focused on highly symmetric molecules such as methane and phosphine, with the corresponding applications at low-T in relation with Titan's atmosphere and at high-T with the production of theoretical line lists for astrophysical opacity calculations10. The study of isotopic H?D and 12C?13C substitutions will be also addressed and carried out by means of symmetry and coordinate transformations11. Finally we hope this work will help refining studies of currently available analyses which are not yet finalized. The modeling of non-LTE emissions accounting for contribution of many fundamental and hot bands could also be possible. Support from PNP (French CNRS national planetology program) is acknowledged.

Research has shown that when Merrill's FirstPrinciples of Instruction are used as part of an instructional strategy, student learning increases. Several articles describe these principles of instruction, including specific methods for implementing this theory. However, because teachers and designers often have little time to design instruction,…

The paper presents a first-principles study of the shear modulus tensor for perfect and imperfect Coulomb solids. Allowance is made for the effects of thermal fluctuations for temperatures up to the melting conditions. The present theory treats the cases of the long-range Coulomb interaction, where volume fluctuations should be avoided in the Ewald sums.

Interfacial water: A firstprinciples molecular dynamics study of a nanoscale water film on salt Li Density functional theory DFT molecular dynamics simulations of a thin 15 Ã? water film on NaCl 001 have interfacial water system. The interaction of the water film with the surface orders the water molecules

First-principles based techniques for the prediction of fixed and rotary wing wake geometry are described. It is demonstrated that fifth order accuracy schemes do substantially better than third order spatial accuracy schemes in capturing the details of the vortex core structure. It is demonstrated that the use of embedded grids can further enhance the resolution of the tip vortex, particularly

Review First-principles and direct design approaches for the control of pharmaceutical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 93 Roger Adams Laboratory, Box C-3, 600 with pharmaceutical crystallization control. This paper provides an overview of recent technological advances

Calculation of solubility in titanium alloys from firstprinciples Roman V. Chepulskii, Stefano solubility in binary alloys based on the statistical-thermodynamic theory of dilute lattice gas. The model dependence determined by a ``low-solubility formation enthalpy". This quantity, directly obtainable from

ccsdÂ­00001055 (version 1) : 22 Jan 2004 Firstprinciples study of the solubility of Zr in Al (Dated: January 22, 2004) The experimental solubility limit of Zr in Al is well-known. Al3Zr has a stable structure DO23 and a metastable one L12 . Consequently there is a metastable solubility limit for which only

"black-box"neural network modelsin that it isable to interpolate and extrapolate much more accurately tool for modeling in engineering applications. Neural networks have typically been used as "blackA Hybrid Neural Network-FirstPrinciples Approach to Process Modeling Dimitris C. Psichogios

The analysis explains the basis set superposition error (BSSE) and fragment relaxation involved in calculating the interaction energies using various firstprinciple theories. Interacting the correlated fragment and increasing the size of the basis set can help in decreasing the BSSE to a great extent.

This paper presents the learning process, oriented to undergraduate students in Naval Architecture, of some procedures for the conceptual design of ships based on firstprinciples. Firstly, considering the points of view of the different stakeholders, the design requirements are identifie d and analyzed, taking into account the relevant physical , economic, technological and social aspects. Based o n this

Epoxide reduction with hydrazine on graphene: A firstprinciples study Min Chan Kim,1,a Gyeong S reduction with hydrazine on a single-layer graphene sheet are examined using quantum mechanical calculations hydrazine or its derivatives. In addition, our calculations suggest that the epoxide reduction by hydrazine

Comparative study of water dissociation on Rh,,111... and Ni,,111... studied with firstprinciples; published online 24 April 2007 The dissociation and formation of water on the Rh 111 and Ni 111 surfaces studied the dissociation of water in the presence of one O atom on Rh 111 , at 0.11 ML coverage

Based on the nonequilibrium Green's function (NEGF) coupled with density function theory (DFT), namely, NEGF-DFT quantum transport theory, we propose an efficient formalism to calculate the transient current of molecular devices under a step-like pulse from firstprinciples. By combining NEGF-DFT with the complex absorbing potential (CAP), the computational complexity of our formalism (NEGF-DFT-CAP) is proportional to O(N) where N is the number of time steps in the time-dependent transient current calculation. Compared with the state-of-the-art algorithm of first-principles time-dependent calculation that scales with at least N2, this order N technique drastically reduces the computational burden making it possible to tackle realistic molecular devices. We have presented a detailed discussion on how to implement this scheme numerically from firstprinciples. To check the accuracy of our method, we carry out the benchmark calculation compared with NEGF-DFT formalism and they agree well with each other. As an application of this method, we investigate the transient current of a molecular device Al-C3-Al from firstprinciples.

In this concept paper, the development of strategies for the integration of first-principles methods with crystallographic database mining for the discovery and design of novel ferroelectric materials is discussed, drawing on the results and experience derived from exploratory investigations on three different systems: (1) the double perovskite Sr(Sb{sub 1/2}Mn{sub 1/2})O{sub 3} as a candidate semiconducting ferroelectric; (2) polar derivatives of schafarzikite MSb{sub 2}O{sub 4}; and (3) ferroelectric semiconductors with formula M{sub 2}P{sub 2}(S,Se){sub 6}. A variety of avenues for further research and investigation are suggested, including automated structure type classification, low-symmetry improper ferroelectrics, and high-throughput first-principles searches for additional representatives of structural families with desirable functional properties. - Graphical abstract: Integration of first-principles methods with crystallographic database mining, for the discovery and design of novel ferroelectric materials, could potentially lead to new classes of multifunctional materials. Highlights: Black-Right-Pointing-Pointer Integration of first-principles methods and database mining. Black-Right-Pointing-Pointer Minor structural families with desirable functional properties. Black-Right-Pointing-Pointer Survey of polar entries in the Inorganic Crystal Structural Database.

We propose a design strategy---based on the coupling of spins, optical phonons, and strain---for systems in which magnetic (electric) phase control can be achieved by an applied electric (magnetic) field. Using first-principles density-functional theory calculations, we present a realization of this strategy for the magnetic perovskite EuTiO3.

We propose a design strategy—based on the coupling of spins, optical phonons, and strain—for systems in which magnetic (electric) phase control can be achieved by an applied electric (magnetic) field. Using first-principles density-functional theory calculations, we present a realization of this strategy for the magnetic perovskite EuTiO3.

Biophysical Modeling of the Temporal Niche: From FirstPrinciples to the Evolution of Activity://www.jstor.org #12;vol. 179, no. 6 the american naturalist june 2012 Biophysical Modeling of the Temporal Niche: From of diurnal versus noc- turnal activity using a biophysical model to evaluate the preferred temporal niche

being used in a wide range of applications due to their light weight and high strength. One. Keywords: Magnesium; Interfaces; Twinning; First-principles calculation Magnesium alloys are increasingly of the current research frontiers on Mg alloys is to understand, estimate and improve their low plastic

Super hard cubic phases of period VI transition metal nitrides: Firstprinciples investigation S July 2008 Keywords: Coatings Elastic properties Hardness Nitrides We report a systematic studyN in rocksalt phase has a bulk modulus of 380 GPa making them candidates for super hardness. Based on the bulk

First-principles studies of iron oxyfluorides in the FeF[subscript 2] rutile framework (FeO[subscript x]F[subscript 2?x], 0?x?1) are performed using density functional theory (DFT) in the general gradient approximation ...

A first-principles model of anomalous thermal transport based on numericalsimulations is presented, with stringent comparisons to experimental datafrom the Tokamak Fusion Test Reactor (TFTR) [Fusion Technol. 21, 1324(1992)]. This model is based on nonlinear gyrofluid simulations, which predictthe fluctuation and thermal transport characteristics of toroidal iontemperature-gradient-driven (ITG) turbulence, and on comprehensive lineargyrokinetic ballooning calculations, which provide...

Based on first-principles calculations we predict a peculiar growth process, where carbon adatoms adsorbed to graphene readily diffuse above room temperature and nucleate segments of linear carbon chains attached to graphene. These chains grow longer on graphene through insertion of carbon atoms one at a time from the bottom end and display a self-assembling behavior. Eventually, two allotropes of carbon,

We provide, by a detailed first-principles investigation, evidence for weak electronic correlations in SrRuO3. The magnetism in SrRuO3, in terms of the equilibrium magnetization and critical temperature, is well described by the generalized gradient approximation. Including Hubbard-type correlations results in worse agreement with experiment.

. To minimize the drive energy for ignition, the imploding shell of DT- fuel needs to be kept as cold the driving energy required for ignition, the imploding DT-capsule needs to be maintained as cold as possible4FPEOS: A First-Principles Equation of State Table of Deuterium for Inertial Confinement Fusion

It has long been recognized that the Earth's outer core must contain a significant amount of light elements, candidates for which have included hydrogen, carbon, silicon, sulfur and oxygen. High-P,T experiments (Jephcoat and Olson, 1987; Mao et al., 1998; Fiquet et al., 2001;Uchida et al., 2001) extended this argument to the inner core on the basis of the equation of state analysis of the hexagonal-closed-pack (hcp) form of pure iron, which concluded that it still has 4-5% excess density compared to the inner core values, although significant extrapolations were usually applied. At present, one of the most popular light-element candidates is sulfur. Therefore, it is crucial to determine the melting behavior of the Fe-FeS binary under core conditions, before models of core formation can be developed. The Fe-FeS binary was known to form a eutectic at low pressures (Usselman, 1975). Sherman (1995), however, suggested the stabilization of an intermediate iron sulfide compound Fe3S with AuCu3 form theoretically, and then Fei et al. (1997) found in the high-P,T experiments that Fe3S2 forms over 14 GPa, and Fe3S and Fe2S further form over 21 GPa (Fei et al., 2000). Fe3S, which is the most iron-rich sulfide compound known to exist, has a tetragonal cell isostructural with the Fe3P structure (space group No.82, Z = 8) and no phase transition has so far been identified up to 80 GPa (Seagle et al., 2006) and even at over 200 GPa (Kuwayama private comm.). These are supportive of an ab initio investigation (Martin et al., 2004), which found that the Fe3P structure is the most stable among fcc, LaF3, YF3 and Fe3P postulations. In this study, we explored higher-pressure phases of Fe3S using first-principles calculations. Comparing enthalpies among candidate structures, we found a new structure which is more stable than the Fe3P structure at the inner core pressures. In our presentation, we will make a detailed report with respect to the new stable structure and discuss phase relations in the Fe-S system. Research supported by JSPS Grant-in-Aid for Scientific Research Grants 20001005 and 21740379 and the Ehime Univ G-COE program “Deep Earth Mineralogy”.

Raman and surface-enhanced Raman (SER) spectroscopies have been applied to the vibrational characterization of diclofenac sodium (DCF-Na). Theoretical calculations (DFT and ab initio) of two DCF-Na conformers have been performed to find the optimized structure and computed vibrational wavenumbers of the most stable one. SER spectra in silver colloid at different pH values have been also recorded and analyzed. Good SER spectra have been obtained in acidic and neutral environments, proving the chemisorption of the DCF-Na molecule on the silver surface. In the investigated pH range the carboxylate anion has been bonded to the silver surface through the lone pair oxygen electrons. The phenyl rings' orientation with respect to the silver surface changed on passing from acidic to neutral pH from a tilted close to flat to a more perpendicular one.

Martensitic phase transformations in TiPd2 and TiPd alloys are studied employing density-functional, first-principles calculations. We examine the transformation of tetragonal C11b TiPd2 to the low-temperature orthorhombic phase (C11b ? oI6), and the transformation of cubic B2 TiPd under orthorhombic (B2?B19) and subsequent monoclinic transformations (B19?B19') as the system is cooled. We employ a theoretical approach based on a phenomenological Landau theory of the structural phase transitions and a mean-field approximation for the free energy, utilizing first-principles calculations to obtain the deformation energy as a function of strains and to deduce parameters for constructing the free energy. The predicted transition temperature for the TiPd2 C11b ? oI6 transition is in good agreement with reported experimental results. To investigate the TiPd B2?B19 transformation, we employ both the Cauchy-Born rule and a soft-mode-based approach, and elucidate the importance of the coupling between lattice distortion and atomic displacements (i.e. shuffling) in the formation of the final structure. The calculated B2?B19 transition temperature for TiPd alloy agrees well with the experimental results. We also find that there exists a very small but finite (0.0005?eV/atom) energy barrier of B19 TiPd under monoclinic deformation for B19?B19' structural phase transformation. PMID:24625683

In this work we report on Car-Parrinello simulations of the divalent calcium ion in water, aimed at understanding the structure of the hydration shell and at comparing theoretical results with a series of recent experiments. Our paper shows some of the progress in the investigation of aqueous solutions brought about by the advent of ab initio molecular dynamics and highlights the importance of accessing subtle details of ion-water interactions from first-principles. Calcium plays a vital role in many biological systems, including signal transduction, blood clotting and cell division. In particular, calcium ions are known to interact strongly with proteins as they tend to bind well to both negatively charged (e.g. in aspartate and glutamate) and uncharged oxygens (e.g. in main-chain carbonyls). The ability of calcium to coordinate multiple ligands (from 6 to 8 oxygen atoms) with an asymmetric coordination shell enables it to cross-link different segments of a protein and induce large conformational changes. The great biochemical importance of the calcium ion has led to a number of studies to determine its hydration shell and its preferred coordination number in water. Experimental studies have used a variety of techniques, including XRD, EXAFS, and neutron diffraction to elucidate the coordination of Ca{sup 2+} in water. The range of coordination numbers (n{sub C}) inferred by X-ray diffraction studies varies from 6 to 8, and is consistent with that reported in EXAFS experiments (8 and 7.2). A wider range of values (6 to 10) was found in early neutron diffraction studies, depending on concentration, while a more recent measurement by Badyal, et al. reports a value close to 7. In addition to experimental measurements, many theoretical studies have been carried out to investigate the solvation of Ca{sup 2+} in water and have also reported a wide range of coordination numbers. Most of the classical molecular dynamics (MD) and QM/MM simulations report n{sub C} in the range of 8 to 10; in general, n{sub C} appears to be highly sensitive to the choice of the ion-water potential used in the calculations. Even ab initio MD simulations have so far obtained conflicting values for n{sub C}. For the structure of the first salvation shell Naor, et al. found n{sub C} = 7 to 8 and a Ca{sup 2+} - oxygen average distance (r{sub Ca-O}) of 2.64 {angstrom}, while Bako, et al. found n{sub C} = 6 and r{sub Ca-O} = 2.45 {angstrom}. In view of the existing controversies, we have carried out extensive Car-Parrinello simulations of Ca{sup 2+} solvation in water, using both a rigid and a flexible water model, up to time scales of 40 ps. Our simulations show variations of coordination numbers from 6, 7 and 8 occurring over intervals of {approx} 0.3/0.4 exchanges/ps, and yielding average coordination numbers of 6.2 and 7 for flexible and rigid water models, respectively. These results are consistent with those reported in recent EXAFS and neutron diffraction experiments. In addition, our calculations show an asymmetric coordination of Ca{sup 2+} to oxygen, similar to the case of Mg{sup 2+}.

In this work, we present firstprinciples calculations based on a full potential linear augmented plane-wave method (FP-LAPW) to calculate structural and electronic properties of CdX and ZnX (X = S, Se, Te) based II-VI chalcogenides. Firstprinciples calculations using the local density approximation (LDA) and the related generalized gradient approximation (GGA) lead to a severe underestimate of the band gap. The proposed model uses various exchange-correlation potentials (LSDA, GGA and MBJLDA) to determine band gaps and structural properties of semiconductors. We show that using modified Becke-Johnson (MBJLDA) density potential leads to a better agreement with experimental data for band gaps of Cd and Zn based semiconductors.

The adhesion of plastics to ceramics is important for many industrial and technological appliations. It is therefore essential to understand the underlying structure and bonding of the polymer and the surface. The aim of this research is to improve plastic adhesion using a multiscale approach. The first step involves the use of density functional calculations to understand the atomic-scale structure and bonding of polymers on surfaces. The plastic of interest is mainly composed of the polymer bisphenol-A-polycarbonate (BPA-PC). The BPA-PC monomer consists of two phenol groups, one propane group and a carbonic acid group. First-principles calculations of the adsorption of these molecules onto the Si(001)-(2x1) dimer surface will be presented. Finally, the incorporation of first-principles data into a coarse-graining method will be discussed.

Hydrogen-helium mixtures at conditions of Jupiter's interior are studied with first-principles computer simulations. The resulting equation of state (EOS) implies that Jupiter possesses a central core of 14-18 Earth masses of heavier elements, a result that supports core accretion as standard model for the formation of hydrogen-rich giant planets. Our nominal model has about 2 Earth masses of planetary ices in the H-He-rich mantle, a result that is, within modeling errors, consistent with abundances measured by the 1995 Galileo Entry Probe mission (equivalent to about 5 Earth masses of planetary ices when extrapolated to the mantle), suggesting that the composition found by the probe may be representative of the entire planet. Interior models derived from this first-principles EOS do not give a match to Jupiter's gravity moment J4 unless one invokes interior differential rotation, implying that jovian interior dynamics has an observable effect on the measured gravity field.

A continuum model of nanowires incorporating surface piezoelectricity is proposed which extends the electric enthalpy energy with surface terms. The corresponding equations are solved by a numerical method using finite elements technique. A methodology is introduced to compute the surface piezoelectric coefficients by first-principles calculations through the Berry phase theory. We provide the e33s, e31s, and e15s piezoelectric coefficients of (101¯0) surfaces for hexagonal wurtzite nanowires made of GaN, ZnO, and AlN. The effective piezoelectric coefficient along the axis of the nanowire is found to increase when the diameter decreases, for the three studied materials. Finally, the solution of the continuum model is compared with large-size first-principles calculations on piezoelectric nanowires.

Calcium-Silicate-Hydrate (C-S-H) is the mineral binding phase of all Portland concrete materials, and the principle source of their strength and stiffness. Despite decades of research, the elastic properties of C-S-H mineral crystals are unknown. Here we investigate two natural analogs of C-S-H, tobermorite and jennite, and characterize their mechanical properties by first-principles calculations. First, we calculate their lattice parameters and elastic constants. Second, we show that in contrast to previous suggestions, for natural tobermorite 11 Å , the mechanically weakest directions are two inclined regions that form a hinge mechanism. By studying bond length changes under deformation in tobermorite 14 Å and jennite, we show that water molecules play a major structural role in defining their elastic properties. Averaged elastic moduli obtained by first-principles calculations of tobermorite 14 Å and jennite compare well with corresponding nanoindentation experiment on C-S-H.

First-principles prediction of lattice thermal conductivity ?L of strongly anharmonic crystals is a long-standing challenge in solid-state physics. Making use of recent advances in information science, we propose a systematic and rigorous approach to this problem, compressive sensing lattice dynamics. Compressive sensing is used to select the physically important terms in the lattice dynamics model and determine their values in one shot. Nonintuitively, high accuracy is achieved when the model is trained on first-principles forces in quasirandom atomic configurations. The method is demonstrated for Si, NaCl, and Cu12Sb4S13 , an earth-abundant thermoelectric with strong phonon-phonon interactions that limit the room-temperature ?L to values near the amorphous limit.

Native point defects in the rutile TiO 2 are studied via first-principles pseudopotential calculations. Except for the two antisite defects, all the native point defects have low formation energies. Under the Ti-rich growth condition, high concentrations of titanium interstitials and oxygen vacancies would form spontaneously in p-type samples; whereas high concentrations of titanium vacancies would form spontaneously in n-type samples regardless of the oxygen partial pressure.

Native point defects in the rutile TiO2 are studied via first-principles pseudopotential calculations. Except for the two antisite defects, all the native point defects have low formation energies. Under the Ti-rich growth condition, high concentrations of titanium interstitials and oxygen vacancies would form spontaneously in p-type samples; whereas high concentrations of titanium vacancies would form spontaneously in n-type samples regardless

We report our first-principles results on point defects in TiO2 in the rutile phase. Both the oxygen vacancy and titanium interstitial are considered. The size effect of the supercell has been examined and the localized state associated with the oxygen vacancy turns out to be sensitive to the supercell size. We find that the oxygen vacancy does not give rise

A first-principles plane-wave pseudopotential method based on density functional theory is used to investigate the concentrations of point defects and their interaction in TiNi. The calculations show that, in the thermal equilibrium state, TiNi develops antisite-type point defect configurations. In accordance with the sequence of the stability of the B2 , B19 , and B19' phases, the concentrations of the

Using the projector-augmented wave method within the generalized gradient approximation, a systematic first-principles calculation for energy vs. volume (E–V) equations of state (EOS’s) and single crystal elastic stiffness constants (cij’s) has been performed for 76 pure elemental solids with face-centered-cubic (fcc), body-centered-cubic (bcc), and hexagonal-close-packed (hcp) crystal structures, wherein the cij’s are determined by an efficient strain–stress method, and the

The C15 NbCr{sub 2} + V Laves phase ternary system is studied by using a first-principles, self-consistent, full-potential total energy method. Equilibrium lattice parameters, cohesive energies, density of states and formation energies of substitutional defects are calculated. Results of all these calculations show that in the C15 NbCr{sub 2} + V compounds, V atoms substitute Cr atoms only.

We present an extensive first-principles study of the interaction between a silicon oxide nanoasperity and a sexithiophene\\u000a monolayer in order to investigate the individual molecular processes responsible for the energy dissipation during atomic\\u000a force microscope (AFM) operation. Our approach includes not only ground-state calculations of the tip–sample interaction,\\u000a but an extensive set of molecular dynamics simulations at room temperature to

First-principle calculations for the diffusion of 3d transition metal (TM) solutes in nickel demonstrate the existence of a higher diffusion energy barrier for solutes with smaller atomic sizes. The calculations reveal that smaller TM atoms are, actually, among the least compressible due to the formation of incompressible solute-host directional bonds. Magnetism is shown to have a profound effect on the

Recently two groups used first-principles computer simulations to model Jupiter’s interior. While both studies relied on the same simulation technique, density functional molecular dynamics, the groups derived very different conclusions. In particular estimates for the size of Jupiter’s core and the metallicity of its hydrogen-helium mantle differed substantially. In this paper, we discuss the differences of the approaches and give an explanation for the differing conclusions.

We present some novel computational methods for scaling up first-principles plane-wave based codes to thousands of processors avoiding communication and latency bottlenecks. This allows our code to scale to more processors and larger systems than previous plane-wave codes that are typically limited in scaling to a few hundred processors. We present performance data for the plane-wave pseudopotential code PARATEC (PARAllel

He defect properties in Sc, Y, Gd, Tb, Dy, Ho, Er and Lu were studied using first-principles calculations based on density functional theory. The results indicate that the formation energy of an interstitial He atom is smaller than that of a substitutional He atom in all hcp rare-earth metals considered. Furthermore, the tetrahedral interstitial position is more favorable than an octahedral position for He defects. The results are compared with those from bcc and fcc metals.

A new, accurate, global, mass-independent, first-principles potential energy surface (PES) is presented for the ground electronic state of the water molecule. The PES is based on 2200 energy points computed at the all-electron aug-cc-pCV6Z IC-MRCI(8,2) level of electronic structure theory and includes the relativistic one-electron mass-velocity and Darwin corrections. For H216O, the PES has a dissociation energy of D0 =

We have performed first-principles molecular dynamics calculations of water adsorption on TiO2 (110). We find that dissociative adsorption occurs at the fivefold-coordinated Ti site resulting in the formation of two types of hydroxyl group. The vibrational spectra calculated from this hydroxylated surface show that a clear stretch frequency is present for only one of these groups, with vibrations from the

A multiscale modeling approach is proposed for calculating energies of tilt-grain boundaries in covalent materials from firstprinciples over an entire misorientation range for given tilt axes. The method uses energies from density-functional calculations for a few key structures as input into a disclination structural-units model. This approach is demonstrated by calculating energies of {l_angle}001{r_angle}-symmetrical tilt-grain boundaries in diamond. {copyright} {ital 1998} {ital The American Physical Society}

The three-dimensional spin-1\\/2 Ising model with multiple-site interactions provides a natural framework for describing the temperature-composition phase diagram of substitutional binary alloys. We have carried out a ``first-principles'' approach to this problem in the following way: (i) The total energy of an A1-xBx alloy in any given substitutional arrangement of A and B on a given lattice is expanded in

Recently two groups used first-principles computer simulations to model Jupiter's interior. While both studies relied on the same simulation technique, density functional molecular dynamics, the groups derived very different conclusions. In particular estimates for the size of Jupiter's core and the metallicity of its hydrogen-helium mantle differed substantially. In this paper, we discuss the differences of the approaches and give an explanation for the differing conclusions.

First-principles electronic structure methods using the generalized gradient approximation have been used to calculate the magnetic groundstate, transition temperature, and thermodynamic properties in spinel MnO_2. This system is of interest because it has both competing ferromagnetic and antiferromagnetic contributions to the exchange coupling and because it is geometrically frustrated. The magnetic interactions were mapped onto a classical Heisenberg model whose

We present a first-principles theory to compute radiation properties of ultra-high quality factor photonic crystal (PC) cavities using a basis of bound PC waveguide states. This method is used to compute the far-field radiation pattern and quality factor of cavity modes $\\sim 100$ times more rapidly than conventional finite-difference time domain methods. Our method provides a simple rule for engineering the PC cavity far-field radiation pattern in high $Q$ cavities.

Using the disordered local moment picture of itinerant magnetism, we present calculations of the temperature and volume dependence of the magnetic moment and spin-spin correlations for fcc Fe in the paramagnetic state. These calculations are based on the parameter-free, firstprinciples approach of local spin density functional theory and the coherent potential approximation is used to treat the disorder associated with the random orientation of the local moments.

Using first-principles total-energy calculations, structural properties of the Si(111)?{31}×?{31}-In reconstruction have been studied. New refined structural model of the reconstruction has been proposed which adopts 17 In atoms and 31 Si atoms. The model is characterized by the reasonably low surface energy and demonstrates good correspondence between simulated and experimental scanning tunneling microscopy images. Calculations reveal semiconducting nature of the model structure in agreement with experiment.

We present a first-principles density-functional study of the structural, electronic, and magnetic properties of the ferroelectric domain walls in multiferroic BiFeO3 . We find that domain walls in which the rotations of the oxygen octahedra do not change their phase when the polarization reorients are the most favorable and of these, the 109° domain wall centered around the BiO plane

We propose a design strategy - based on the coupling of spins, optical\\u000aphonons, and strain - for systems in which magnetic (electric) phase control\\u000acan be achieved by an applied electric (magnetic) field. Using first-principles\\u000adensity-functional theory calculations, we present a realization of this\\u000astrategy for the magnetic perovskite EuTiO$_3$.

Ballistic phonon thermal conductances for graphene nanoribbons are investigated using first-principles calculations with the density functional perturbation theory and the Landauer theory. The phonon thermal conductance per unit width for GNR is larger than that for graphene and increases with decreasing ribbon width. The normalized thermal conductances with regard to a thermal quantum for GNRs are higher than those for the single-walled carbon nanotube that have circumferential lengths corresponding to the width of GNR.

This work is a study exploring the extent of suitability of static first-principles calculations for studying diffusion in metallic systems. Specifically, vacancy-mediated volume diffusion in pure elements and alloys with dilute concentration of impurities is studied. A novel procedure is discovered for predicting diffusion coefficients that overcomes the shortcomings of the well-known transition state theory, by Vineyard. The procedure that

We report the results of a comparative study of pentaerythritol tetranitrate (PETN) at high compression using classical reactive interatomic potential ReaxFF and first-principles density functional theory (DFT). Lattice parameters of PETN I, the ground state structure at ambient conditions, is obtained by ReaxFF and two different density functional methods (plane wave and LCAO pseudopotential methods) and compared with experiment. Calculated

Possible ferromagnetic and ferroelectric phases are explored for bismuth transition-metal oxides with double-perovskite structure A2BB?O6 on the basis of first-principles calculations within the local spin-density approximation (LSDA) and generalized gradient approximation (GGA). It is found that a lattice instability of the cubic to a non-centrosymmetric phase always happens in the all cases of lead and bismuth perovskite oxides with the

We propose a first-principles based method for calculating the electronic structure and total energy of solids in an intermediate-valence configuration. The method takes into account correlation effects (d-f Coulomb interaction) and many-body renormalization of the effective hybridization parameter of the f system. As an example, the formation of a pressure-induced intermediate-valence state in Yb is considered and its electronic structure

First-principles modeling of ferroelectric capacitors presents several technical challenges due to the coexistence of metallic electrodes, long-range electrostatic forces, and short-range interface chemistry. Here we show how these aspects can be efficiently and accurately rationalized by using a finite-field density-functional theory formalism in which the fundamental electrical variable is the displacement field D . By performing calculations on model Pt\\/BaTiO3\\/Pt

Based on firstprinciples calculations, we investigate two probable types of deactivation mechanisms that hinder current efforts of doping ZnO p-type. (i) Passivation by Hydrogen. H prefers to bind with NO at the anti-bonding site and form NO–H complexes with a binding energy of about 1eV. (ii) Passivation by the formation of substitutional diatomic molecules (SDM). Carbon impurities and excess

In this work we simulate the diffraction peak intensities of He beams scattered on the MgO(100) surface from firstprinciples. It turns out that diffraction peak intensities are extremely sensitive to the quality of the potential describing the He-MgO surface interaction. Achieving the required accuracy in firstprinciples calculations is very challenging indeed. The present work describes a firstprinciples protocol able to achieve very high accuracy for reasonable computational cost. This method is based on periodic local second-order Møller-Plesset perturbation theory where systematic corrections for basis set truncation and for high-order electronic correlation are introduced using coupled cluster calculations on finite model systems mimicking the target system. For the He-MgO system the requirements with respect to the level of theory are very high; it turns out that contributions from connected quadruple excitations are non-negligible. Here we demonstrate that using this protocol, it is possible to reach the accuracy in the He-MgO potential that is required to predict the observed He diffraction peak intensities. PMID:24985572

An approach to access the stability of oxides growing on top of a metal support is presented. In combination with first-principles calculations, it allows to predict the stable structures as a function of the thickness of the evaporated metal ad-layer and as a function of the oxygen pressure. The ideas are applied to thin vanadium oxide films growing on Pd(1 1 1). To investigate the stability of these oxide films, first-principles calculations for more than 50 thin films of V xO y on Pd were performed at varying stoichiometry and coverage. The general principles determining the growth of thin vanadium oxide films on Pd(1 1 1) are discussed, and the experimental results are interpreted in the light of the first-principles calculations. At 1 ML vanadium coverage, a complicated succession of structures is predicted by the calculations. At high oxygen pressure bulk like V 2O 3 phases are stable. At lower oxygen pressure, however, a surface stabilised (2×2) reconstruction with a formal stoichiometry of V 2O 3 is predicted, and rectangular and hexagonal vanadium-dioxide phases are expected to grow. At very low oxygen pressures, first the vanadium-dioxide phases and then the surface V 2O 3 phase decompose and the liberated V atoms move subsurface. These predictions are in good general agreement with experiment. An important result of the study is that the metal surface stabilises thin films which have no equivalent bulk phases.

We report on a first-principles investigation of transient heat current through molecular devices under steplike pulse of external and gate voltages. Using the nonequilibrium Green's function (NEGF) approach, an exact solution of transient heat current is obtained that goes beyond the wide-band limit. Combining with density-functional theory (DFT), we propose a time-dependent NEGF-DFT formalism to study the transient heat current under a steplike pulse for molecular devices from firstprinciples. Anticipating the huge computational cost in the transient regime, we develop an algorithm to speed up the calculation using the complex absorbing potential (CAP). By adding the CAP to replace the Hamiltonian of leads, the effective self-energy of the Green's function becomes independent of energy, allowing analytic calculation of the triple integrations in the exact solution of transient heat current using the theorem of residue. With this linear scaling algorithm, the computational complexity is greatly reduced, and a first-principles calculation of transient heat current of molecular devices becomes possible. As an example, we apply our NEGF-DFT-CAP formalism for a molecular device, the Di-thiol benzene molecule connected by two semi-infinite aluminum leads, and we calculate the transient heat current under an upward gate voltage pulse. The enhancement of heat current is observed.

The structural phase transitions and the fundamental band gaps of MgxZn1 xO alloys are investigated by detailed first-principles calculations in the entire range of Mg concentrations x, applying a multiple-scattering theoretical approach (Korringa-Kohn-Rostoker method). Disordered alloys are treated within the coherent-potential approximation. The calculations for various crystal phases have given rise to a phase diagram in good agreement with experiments and other theoretical approaches. The phase transition from the wurtzite to the rock-salt structure is predicted at the Mg concentration of x=0.33, which is close to the experimental value of 0.33 0.40. The size of the fundamental band gap, typically underestimated by the local-density approximation, is considerably improved by the self-interaction correction. The increase in the gap upon alloying ZnO with Mg corroborates experimental trends. Our findings are relevant for applications in optical, electrical, and, in particular, in magnetoelectric devices.

PHYSICAL REVIEW B 89, 035120 (2014) Electronic stopping power from first-principles calculations electronic stopping power Se of energetic ions in graphitic targets from firstprinciples. By treating core into the dependence of the electronic stopping power Se on projectile velocity have been obtained with the explicit

Measurements of the dielectric (or impedance) properties of cells can be used as a general characterization and diagnostic tool. In this paper, we describe a novel impedance spectroscopy technique for the analysis of single biological cells in suspension. The technique uses maximum length sequences (MLS) for periodic excitation signal in a microfluidic impedance cytometer. The method allows multi-frequency single cell impedance measurements to be made in a short time period (ms). Spectral information is obtained in the frequency domain by applying a fast M-sequence transform (FMT) and fast Fourier transform (FFT) to the time domain response. Theoretically, the impedance is determined from the transfer function of the system when the MLS is a current excitation. The order of the MLS and sampling rate of A/D conversion are two factors that determine the bandwidth and spectral accuracy of the technique. Experimentally, the applicability of the technique is demonstrated by characterizing the impedance spectrum of red blood cells (RBCs) in a microfluidic cytometer. The impedance is measured within 1 ms at 512 discrete frequencies, evenly distributed in the range from 976.56 Hz to 500 kHz. The measured spectrum shows good agreement with simulations.

Understanding the structure of water near cell membranes is crucial for characterizing water-mediated events such as molecular transport. To obtain structural information of water near a membrane, it is useful to have a surface-selective technique that can probe only interfacial water molecules. One such technique is vibrational sum-frequency generation (VSFG) spectroscopy. As model systems for studying membrane headgroup/water interactions, in this paper we consider lipid and surfactant monolayers on water. We adopt a theoretical approach combining molecular dynamics simulations and phase-sensitive VSFG to investigate water structure near these interfaces. Our simulated spectra are in qualitative agreement with experiments and reveal orientational ordering of interfacial water molecules near cationic, anionic, and zwitterionic interfaces. OH bonds of water molecules point toward an anionic interface leading to a positive VSFG peak, whereas the water hydrogen atoms point away from a cationic interface leading to a negative VSFG peak. Coexistence of these two interfacial water species is observed near interfaces between water and mixtures of cationic and anionic lipids, as indicated by the presence of both negative and positive peaks in their VSFG spectra. In the case of a zwitterionic interface, OH orientation is toward the interface on the average, resulting in a positive VSFG peak.

The present study reinvestigates the Al-Ce and Al-Nd phase diagrams and reoptimizes their thermodynamics using the CALPHAD\\u000a method. First-principles energy calculations play an important role in terms of sublattice formalism and phase-stability prediction,\\u000a demonstrating that they should be effectively integrated into experimental investigations and thermodynamic assessments. Specifically,\\u000a current experimental results and theoretical calculations show that Al2Nd (or Al2Ce) should be

This paper performs first-principles calculations to study the structural, mechanical and electronic properties of the spinels ZnAl2O4, ZnGa2O4 and ZnCr2O4, using density functional theory with the plane-wave pseudopotential method. Our calculations are in good agreement with previous theoretical calculations and the available experimental data. The studies in this paper focus on the evolution of the mechanical properties of ZnAl2O4, ZnGa2O4

We investigated theoretically the adsorption of individual Mg atoms on single-walled carbon nanotubes (SWCNTs) by first-principles method within density functional theory in order to clarify the binding energies and the electronic structures of Mg atoms contact with SWCNTs. Our results suggest that the interaction of Mg atom adsorbed on pristine SWCNTs, which is normally very weak, can be enhanced upon functionalization of SWCNTs by B- or N-doping. Especially, the B-doping increases dramatically the binding energies of Mg-adsorbed on both armchair and zigzag SWCNTs.

This work is a study exploring the extent of suitability of static first-principles calculations for studying diffusion in metallic systems. Specifically, vacancy-mediated volume diffusion in pure elements and alloys with dilute concentration of impurities is studied. A novel procedure is discovered for predicting diffusion coefficients that overcomes the shortcomings of the well-known transition state theory, by Vineyard. The procedure that evolves from Eyring's reaction rate theory yields accurate diffusivity results that include anharmonic effects within the quasi-harmonic approximation. Alongside, the procedure is straightforward in its application within the conventional harmonic approximation, from the results of static first-principles calculations. To prove the extensibility of the procedure, diffusivities have been computed for a variety of systems. Over a wide temperature range, the calculated self-diffusion and impurity diffusion coefficients using local density approximation (LDA) of density functional theory (DFT) are seen to be in excellent match with experimental data. Self-diffusion coefficients have been calculated for: (i) fcc Al, Cu, Ni and Ag (ii) bcc W and Mo (v) hcp Mg, Ti and Zn. Impurity diffusion coefficients have been computed for: (i) Mg, Si, Cu, Li, Ag, Mo and 3d transition elements in fcc Al (ii) Mo, Ta in bcc W and Nb, Ta and W in bcc Mo (iii) Sn and Cd in hcp Mg and Al in hcp Ti. It is also an observation from this work, that LDA does not require surface correction for yielding energetics of vacancy-containing system in good comparison with experiments, unlike generalized gradient approximation (GGA). It is known that first-principles' energy minimization procedures based on electronic interactions are suited for metallic systems wherein the valence electrons are freely moving. In this thesis, research has been extended to study suitability of first-principles calculations within LDA/GGA including the localization parameter U, for Al system with transition metal solutes, in which charges are known to localize around the transition metal element. U parameter is determined from matching the diffusivities of 3d transition metal impurity in aluminum with reliable experimental data. The effort yielded activation energies in systematic agreement with experiments and has proved useful in obtaining insights into the complex interactions in these systems. Besides the prediction of diffusion coefficients, this research has been helpful in understanding the physics underlying diffusion. Within the scope of observations from the systems studied, certain diffusion related aspects that have been clarified are: (i) cause for non-Arrnenius' nature of diffusion plots (ii) definitions of atom migration properties (iii) magnitude and sign of diffusion parameters enthalpy and entropy of formation and migration and characteristic vibrational frequency (iv) trends in diffusivities based on activation energy and diffusion prefactor (vi) cause for anomalous diffusion behavior of 3d transition metals in Al, and their magnetic nature (vii) contributions from electronic contributions to curvature at very high temperatures of bcc refractory elements (viii) temperature dependence of impurity diffusion correlation factors. Finally, the double-well potential of diffusion by vacancy mechanism has been calculated from first-principles. This aided calculation of entropy of migration and thus free energy of migration along with characteristic vibrational frequency. Also for the first time, temperature dependence of enthalpy of migration and thus atom jump frequency has been accurately predicted. From the broad perspective of predicting diffusion coefficients from computational methodologies, it can be stated as a result of this work that: static first-principles extend an irreplaceable contribution to the future of diffusion modeling. The procedure obviated the use of (i) redundant approximations that limit its accuracy and (ii) support from other computational techniques that restrict its extensibility due to insufficient i

Carrier compensation in semi-insulating CdTe has been attributed to the compensation of surplus shallow acceptors by deep donors, usually assumed to be Te antisites. However, our first-principles calculations show that intrinsic defects should not have a significant effect on the carrier compensation due either to lack of deep levels near midgap or to low defect concentration. We demonstrate that an extrinsic defect, OTe-H complex, may play an important role in the carrier compensation in CdTe because of its amphoteric character and reasonably high concentration. Our findings have important consequences for improving device performance in CdTe-based radiation detectors and solar cells.

The present paper reports the calculated vibrational and elastic properties of some two dimensional carbon allotropes such as graphene, ?-, ?- and ?-graphynes using firstprinciples density functional theory. The phonon modes of graphynes show quite distinct behavior than graphene and have real frequency throughout the Brillouin zone thus indicating dynamically stable structures. The out of plane, ZA mode is more dispersive in the case of graphynes. We have discussed the implications of phonon modes to the thermal conductance in graphynes and graphene. We have also calculated the elastic constants for graphene and graphynes. Calculated elastic constants of graphynes show more anisotropic conformer nature than graphene.

The atomic-scale friction of the fluorographene (FG)/MoS2 heterostructure is investigated using first-principles calculations. Due to the intrinsic lattice mismatch and formation of periodic Moiré patterns, the potential energy surface of the FG/MoS2 heterostructure is ultrasmooth and the interlayer shear strength is reduced by nearly two orders of magnitude, compared with both FG/FG and MoS2/MoS2 bilayers, entering the superlubricity regime. The size dependency of superlubricity is revealed as being based on the relationship between the emergence of Moiré patterns and the lattice mismatch ratio for heterostructures.

The ground state electronic structures of the actinide oxides AO, A{sub 2}O{sub 3} and AO{sub 2} (A=U, Np, Pu, Am, Cm, Bk, Cf) are determined from first-principles calculations using the self-interaction corrected local spin-density approximation. Our study reveals a strong link between preferred oxidation number and degree of localization. The ionic nature of the actinide oxides emerges from the fact that those oxides where the ground state is calculated to be metallic do not exist in nature, as the corresponding delocalized f-states favour the accommodation of additional O atoms into the crystal lattice.

Using first-principles calculations, we investigate the electronic structures and binding properties of nicotine and caffeine adsorbed on single-walled carbon nanotubes to determine whether CNTs are appropriate for filtering or sensing nicotine and caffeine molecules. We find that caffeine adsorbs more strongly than nicotine. The different binding characteristics are discussed by analyzing the modification of the electronic structure of the molecule-adsorbed CNTs. We also calculate the quantum conductance of the CNTs in the presence of nicotine or caffeine adsorbates and demonstrate that the influence of caffeine is stronger than nicotine on the conductance of the host CNT.

The equation of state of TcC with rocksalt structure is investigated by means of first-principles density functional theory calculations combined with the quasi-harmonic Debye model in which the phononic effects are considered. Particular attention is paid to the predictions of the compressibility, the isothermal bulk modulus and its first pressure derivative which play a central role in the formulation of approximate equations of state for the first time. The properties of TcC with rocksalt structure are summarized in the pressure range of 0-80 GPa and the temperature up to 2500 K.

We report firstprinciples density functional calculations for 5,6-dihydroxyindole-2-carboxylic acid (DHICA) and several reduced forms. DHICA and 5,6-dihydroxyindole (DHI) are believed to be the basic building blocks of the eumelanins. Our results show that carboxylation has a significant effect on the physical properties of the molecules. In particular, the relative stabilities and the HOMO-LUMO gaps (calculated with the $\\Delta$SCF method) of the various redox forms are strongly affected. We predict that, in contrast to DHI, the density of unpaired electrons, and hence the ESR signal, in DHICA is negligibly small.

First-principles calculations of the crystalline vibrations of a lactose monohydrate crystal in the terahertz (THz) region were performed using periodic density functional theory calculations. The calculated vibrational modes in the THz region were derived from group motions with different sizes: molecules of lactose and crystal water, pyranose rings, and intramolecular frames. The intermolecular modes with large vibrational amplitude of lactose of 17.5-100.6 cm-1 and of crystal-water of 136.1-237.7 cm-1 were clearly separated. This article especially refers to the intermolecular vibrational modes of crystal water with the THz absorption, which provide detectable spectral features of hydrated crystals.

The effect of substitutional doping of fluorographene with boron and nitrogen atoms on its electronic and magnetic properties is investigated using first-principles calculations. It is found that boron dopants can be readily incorporated in the fluorographene crystal where they act as shallow acceptors and cause hole doping, but no changes in the magnetic properties are observed. Nitrogen dopants act as deep donors and give rise to a magnetic moment, but the resulting system becomes chemically unstable. These results are opposite to what was found for substitutional doping of graphane, i.e., hydrogenated graphene, in which case B substituents induce magnetism and N dopants do not.

The process of hydrogen depassivation of the acceptor by can convert the as-grown high-resistivity -doped into a - conducting material. A first-principles study on the process will be presented. The formation energies of various complex of impurities and point defects have been calculated and compared. The diffusion barriers of the hydrogen atom in the doped GaN have been obtained by the Nudge-Elastic-Band method. The results explain successfully the experimental observation that the hole concentration has been significantly enhanced in a Be-implanted Mg-doped GaN.

From first-principles calculations, we proposed a silicon germanide (SiGe) analog of silicene. This SiGe monolayer is stable and free from imaginary frequency in the phonon spectrum. The electronic band structure near the Fermi level can be characterized by Dirac cones with the Fermi velocity comparable to that of silicene. The Ge and Si atoms in SiGe monolayer exhibit different tendencies in binding with hydrogen atoms, making sublattice-selective hydrogenation and consequently electron spin-polarization possible. PMID:23945421

From first-principles calculations, we proposed a silicon germanide (SiGe) analog of silicene. This SiGe monolayer is stable and free from imaginary frequency in the phonon spectrum. The electronic band structure near the Fermi level can be characterized by Dirac cones with the Fermi velocity comparable to that of silicene. The Ge and Si atoms in SiGe monolayer exhibit different tendencies in binding with hydrogen atoms, making sublattice-selective hydrogenation and consequently electron spin-polarization possible.

We present a first-principles study of the coherent charge transport properties of bistable [2]catenane molecular monolayers sandwiched between Au(111) electrodes. We find that conduction channels around the Fermi level are dominated by the two highest occupied molecular orbital levels from tetrathiafulvalene (TTF) and dioxynaphthalene (DNP) and the two lowest unoccupied molecular orbital levels from tetracationic cyclophane (CBPQT4+), and the OFF to ON switching results from the energetic shifts of these orbitals as CBPQT4+ moves from TTF to DNP. We show that the superposition principle can be adopted for predicting the function of the composite device.

We have studied selected DNA base molecules, such as guanine, cytosine, adenine, and thymine, and methylated DNA base molecules from first-principles. The impact of methylation and the rearrangement of the hydrogen atoms of the DNA base molecules on the geometries and the electronic properties are explained with the bond orders, the steric effects, and the molecular topologies. A DNA base molecule without methylation and a corresponding methylated DNA base molecule with the same bond order are expected to have similar HOMO-LUMO energy gaps.

The properties of compressed liquid hydrogen, the most abundant fluid in the universe, have been investigated by means of first-principles molecular dynamics at pressures between 75 and 175 GPa and temperatures closer to the freezing line than so far reported in shock-wave experiments. Evidence for a liquid–liquid transition between a molecular and a dissociated phase is provided. The transition is accompanied by a 6% increase in density and by metallization. This finding has important implications for our understanding of the interiors of giant planets and supports predictions of a quantum fluid state at low temperatures. PMID:12626753

First-principles simulations of Ca-based metallic glass-forming alloys yield sample amorphous structures whose structures can be compared to experiment and whose properties can be analyzed. In an effort to understand and control ductility, we investigate the elastic moduli. Calculated Poisson ratios depend strongly on alloying elements in a manner that correlates with ionicity (charge transfer). Consequently, we predict that alloying Ca with Mg and Zn should result in relatively ductile glasses compared to alloying with Ag, Cu, or Al. Experimental observations validate these predictions.

Using first-principles density functional calculations and the generalized gradient approximation functional including the on-site Coulomb interaction of 4f orbitals, we show that ferroelectricity can be induced by appropriate epitaxial tensile strain in GdN with a simple rock-salt structure, and that the polarization is sensitive to the strain. The calculated phonon spectra of strained GdN also confirm the existence of ferroelectric polarization. In addition, the electronic structure and magnetic properties of strained GdN as a function of strain are investigated. The present work opens up the possibility of epitaxially tensioned GdN thin films as potential multiferroics. PMID:21625033

The rapid solidification processes of Ca50Mg20Cu30 liquid alloy have been simulated by firstprinciple molecular dynamics simulation based on the density functional theory. The local structural evolution of the alloy is analysed using Honeycutt Andersen (HA) bond-type index and bond-angle distribution methods. The electronic properties of this amorphous solid are also studied. The simulated coordination numbers are very close to the theoretical values according to the efficient cluster packing model (ECP) model. The interaction between Ca-Cu atomic pairs is strongest in this alloy. The HA bond-type result shows that a large quantity of pentagonal bipyramids are formed in undercooled alloy liquid and become most common polyhedral local structures of the amorphous solid, which suppress the crystallization and increase the glass forming ability of Ca-Mg-Cu alloy. The bond-angle distribution indicates that the close packing of the three neighbor atoms and the pentagon configurations become the primary short range order (SRO) as temperature decreases. The electronic density demonstrates that the covalent bond of Ca-Mg, Ca-Cu, Mg-Cu, and Cu-Cu pairs is existed in this alloy. This chemical SRO also benefits the glass transition.

Linear optical properties of regio-regular-poly(3-hexythiophene) (rr-P3HT) and regio-regular-poly(3-hexyselenophene) (rr-P3HS) are investigated in relation to their anisotropic crystal structure by means of first-principles density functional calculations. The optical spectra are evaluated by calculating its dielectric functions, focusing on the frequency dependence of the imaginary part. The optical transition along the ? conjugation-connecting backbone direction is found to be the most significant at the band edges. A group-theoretical analysis of the matrix elements is given to explain the interband transitions. The optical spectra, electronic structures, and structural stabilities are calculated using the all-electron full-potential linearized augmented plane wave (FLAPW) method within the local-density approximation. We proposed several possible crystal structures of rr-P3HT and performed structural optimizations to determine a stable structure. Comparing the total energy differences among these relaxed structures, a base-centered monoclinic structure belonging to the space group A2 is found to be the most stable structure. In the electronic structure, C and S orbitals belonging to polythiophene backbones are the biggest contributors at the valence band maximum and conduction band minimum, but there is almost no contribution from the hexyl side chains. Last, the differences in electronic and optical properties between rr-P3HT and rr-P3HS are discussed.

In this work, the state-of-the-art infrared variable angle spectroscopic ellipsometry (IR-VASE) and first-principles molecular dynamics (FPMD) method were combined to obtain the infrared dielectric functions of MgO crystal in the spectral range 300-1000 cm-1 and for temperatures up to 1950 K. The IR-VASE can measure the infrared dielectric functions of MgO crystal at temperatures ranging from 300 to 573 K and reproduce previous infrared-reflectivity experiments. As temperature increases, it demonstrates that the amplitude of dominant absorption peak centered around 400 cm-1 reduces, the width broadens, and the position shifts to longer wavelength. Besides ellipsometry study, the FPMD method was implemented, seeking to theoretically predict the infrared spectra of MgO crystal at elevated temperatures. Comparing with experimental measurements, the FPMD method can reproduce the essential feature of ellipsometry and previous infrared-reflectivity experiments even at elevated temperatures, though with some deviations in predicting the exact position and amplitude of dominant absorption peak. On the other hand, the FPMD method can predict the temperature effect on the infrared dielectric functions of MgO crystal, e.g., redshift and broadened absorption peak with increasing temperature.

The adsorption and dissociation of three carbonyl compounds, formaldehyde, acetaldehyde, and acetone, on the magnesium oxide nanosurface, consisting of four stacked (MgO)3 hexagons, is investigated by firstprinciples density functional theory (DFT). In the case of formaldehyde, strongly chemisorbed species, with carboxylate-like structures, are initially formed. These may subsequently undergo heterolytic cleavage of an aldehyde C-H bond to form formate ions involving a surface oxide ion and a hydride ion adsorbed over the magnesium dication [(MgH+)(HCOO-)]. For acetaldehyde, besides this reaction leading to the formation of acetate, the methyl hydrogen of the adsorbed species also tends to attach itself to a surface oxide ion, yielding surface hydroxyl ions and adsorbed [CH2=C(H)OMg]+. These results are in accord with our previous experimental and theoretical results. In particular, the shift of the aldehyde C-H vibration band to higher frequency and the appearance of OH bands in the infrared spectrum are clearly accounted for. For acetone, the mechanism is found to be similar, i.e., a methyl hydrogen shift to yield surface enolate. Again, this is in agreement with experimental studies. PMID:17181243

The electronic structures of nanometre-sized nickel silicide systems, Ni(2)Si and NiSi, have been studied by energy-loss near-edge structure (ELNES) and first-principles band structure calculations. Experimental ELNES of Ni L(3)- and Si L(2,3)-edges could be explained well using theoretical spectra calculated for the ground state without the core hole, suggesting metallic properties for both silicides. It was shown that a slight difference in ELNES spectra of Ni(2)Si and NiSi comes from the coupling among the Ni d and Si p, d states in the unoccupied bands. The density of states and the contour plots of all the valence electron densities for Ni(2)Si, NiSi together with NiSi(2) show that Ni(2)Si has the bond with the strongest covalent character between Ni and Si atoms and the most transition metal-like character of the Ni 3d band among the three silicides. PMID:17697750

Structural, electronic and optical properties of binary BeTe and CdS compounds and their (BeTe)n/(CdS)n superlattices (SLs) are investigated using the first-principles full potential linear muffin-tin orbitals method (FP-LMTO). The exchange-correlation potential is treated with the local density approximation of Perdew and Wang (LDA-PW). The ground-state properties are determined for the bulk materials (BeTe, CdS, and (BeTe)n/(CdS)n) in cubic phase. The calculated structural properties of BeTe and CdS compounds are in good agreement with available experimental and theoretical data. It is found that BeTe exhibit an indirect fundamental band gap and CdS and their superlattices (SLs) exhibit a direct fundamental band gap, which might make (BeTe)n/(CdS)n superlattices (SLs) materials promising and useful for optoelectronic applications. The fundamental band gap decreases with increasing the number of monolayer n.

In this paper, we report the by first-principles predicted properties of the recently discovered magnetic MAX phase Mn2GaC. The electronic band structure and vibrational dispersion relation, as well as the electronic and vibrational density of states, have been calculated. The band structure close to the Fermi level indicates anisotropy with respect to electrical conductivity, while the distribution of the electronic and vibrational states for both Mn and Ga depend on the chosen relative orientation of the Mn spins across the Ga sheets in the Mn-Ga-Mn trilayers. In addition, the elastic properties have been calculated, and from the five elastic constants, the Voigt bulk modulus is determined to be 157 GPa, the Voigt shear modulus 93 GPa, and the Young's modulus 233 GPa. Furthermore, Mn2GaC is found relatively elastically isotropic, with a compression anisotropy factor of 0.97, and shear anisotropy factors of 0.9 and 1, respectively. The Poisson's ratio is 0.25. Evaluated elastic properties are compared to theoretical and experimental results for M2AC phases where M = Ti, V, Cr, Zr, Nb, Ta, and A = Al, S, Ge, In, Sn.

This work presented theoretical studies of structures, energies and properties of armchair carbon nanotubes (CNTs) upon the silicon substitutional doping by using first-principle calculations. The doping effects on quantitative description from viewpoint of the pi-orbital axis vector theory, relative stability, defect formation energy, electronic structure, nonlinear optical property and aromaticity of the tubes has been addressed systemically and in details. The obtained pyramidalization angles of the silicon are much larger than those of carbon according to the pi-orbital axis vector analysis. The results of defect formation energy suggest that the Si-doping would be contained easier in small CNTs. A quantitative relation about the curvature-dependent defect formation energy is obtained. The silicon atoms exhibit large distributions for the frontier molecular orbital of doped tubes. As for the nonlinear optical property, the hyperpolarizability of the tubes is dramatically enhanced upon silicon defect. The doping effect on the aromaticity is also studied. It is found that the aromaticity/anti-aromaticity transition is even occurred at the selected positions based on the probe of nuclear independent chemical shift.

We present the results of a first-principles study of the electronic and structural properties of binary CdTe and ZnTe compounds and their (CdTe)n/(ZnTe)n superlattices (SLs). The computational method is based on the full-potential linear muffin tin orbitals method (FP-LMTO) augmented by a plane-wave basis (PLW). The exchange and correlation energy is described in the local density approximation (LDA) using the Perdew-Wang parameterization including a generalized gradient approximation (GGA). The calculated structural properties of CdTe and ZnTe compounds are in good agreement with available experimental and theoretical data. We have also carried out band-structure calculations for the binary CdTe and ZnTe compounds and their (CdTe)n/(ZnTe)n superlattices (SLs). From the results of the electronic properties, we find that the parent material CdTe and ZnTe and their superlattices have a direct band gaps. The fundamental band gap decreases with increasing the number of monolayer n.

We give a theoretical framework to obtain a low-energy effective theory of quantum chromodynamics (QCD) towards a first-principle derivation of confinement/deconfinement and chiral-symmetry breaking/restoration crossover transitions. In fact, we demonstrate that an effective theory obtained using simple but nontrivial approximations within this framework enables us to treat both transitions simultaneously on equal footing. A resulting effective theory is regarded as a modified and improved version of nonlocal Polyakov-loop extended Nambu-Jona-Lasinio (nonlocal PNJL) models proposed recently by Hell, Roessner, Cristoforetti, and Weise, and Sasaki, Friman, and Redlich, extending the original (local) PNJL model by Fukushima and others. A novel feature is that the nonlocal NJL coupling depends explicitly on the temperature and Polyakov loop, which affects the entanglement between confinement and chiral-symmetry breaking, together with the cross term introduced through the covariant derivative in the quark sector considered in the conventional PNJL model. The chiral-symmetry breaking/restoration transition is controlled by the nonlocal NJL interaction, while the confinement/deconfinement transition in the pure gluon sector is specified by the nonperturbative effective potential for the Polyakov loop obtained recently by Braun, Gies, Marhauser, and Pawlowski. The basic ingredients are a reformulation of QCD based on new variables and the flow equation of the Wetterich type in the Wilsonian renormalization group. This framework can be applied to investigate the QCD phase diagram at finite temperature and density.

In this work, the state-of-the-art infrared variable angle spectroscopic ellipsometry (IR-VASE) and first-principles molecular dynamics (FPMD) method were combined to obtain the infrared dielectric functions of MgO crystal in the spectral range 300-1000 cm(-1) and for temperatures up to 1950 K. The IR-VASE can measure the infrared dielectric functions of MgO crystal at temperatures ranging from 300 to 573 K and reproduce previous infrared-reflectivity experiments. As temperature increases, it demonstrates that the amplitude of dominant absorption peak centered around 400 cm(-1) reduces, the width broadens, and the position shifts to longer wavelength. Besides ellipsometry study, the FPMD method was implemented, seeking to theoretically predict the infrared spectra of MgO crystal at elevated temperatures. Comparing with experimental measurements, the FPMD method can reproduce the essential feature of ellipsometry and previous infrared-reflectivity experiments even at elevated temperatures, though with some deviations in predicting the exact position and amplitude of dominant absorption peak. On the other hand, the FPMD method can predict the temperature effect on the infrared dielectric functions of MgO crystal, e.g., redshift and broadened absorption peak with increasing temperature. PMID:25217943

We perform the first-principles calculations within the framework of density functional theory to determine the electronic structure and optical properties of MgxZn1−xS bulk crystal. The results indicate that the electronic structure and optical properties of MgxZn1−xS bulk crystal are sensitive to the Mg impurity composition. In particular, the MgxZn1−xS bulk crystal displays a direct band structure and the band gap increases from 2.05 eV to 2.91 eV with Mg dopant composition value x increasing from 0 to 0.024. The S 3p electrons dominate the top of valence band, while the Zn 4s electrons and Zn 3p electrons occupy the bottom of conduction band in MgxZn1−xS bulk crystal. Moreover, the dielectric constant decreases and the optical absorption peak obviously has a blue shift. The calculated results provide important theoretical guidance for the applications of MgxZn1−xS bulk crystal in optical detectors.

The properties of defects in materials are crucial in order to determine their performance and behavior, especially at extreme conditions (at high temperature, under irradiation or with other types of constraints). Formation and migration energies of defects are studied routinely using first-principles calculations. However, most of the time, they are studied by static zero-temperature calculations, and the entropic contributions to the free energies are completely neglected. In this paper we address the first-principles calculation of the vibrational part of the free energies of formation and migration of silicon and carbon interstitials in silicon carbide. The latter is an important material for high-temperature applications. We find that formation free enthalpies can vary by up to 1 eV, in the range from 0 to 2000 K, while migration free energies vary by only a few tenth of an electron volt. Our results give us not only the activation energies for diffusion but also diffusion prefactors. The comparison with experimental results shows good agreement for carbon self-diffusion while for silicon self-diffusion our results underestimate by three orders of magnitude the experimental values, suggesting that defects other than the interstitials are the dominant diffusing species. As a last point, in the light of our results, we discuss empirical models concerning diffusion coefficients and entropy-energy relations.

A series of firstprinciples Monte Carlo simulations in the isobaric-isothermal ensemble were carried out for liquid water at ambient conditions (T = 298 K and p = 1 atm). The Becke-Lee-Yang-Parr (BLYP) exchange and correlation energy functionals and norm-conserving Goedecker-Teter-Hutter (GTH) pseudopotentials were employed with the CP2K simulation package to examine systems consisting of 64 water molecules. The fluctuations in the system volume encountered in simulations in the isobaric-isothermal ensemble requires a reconsideration of the suitability of the typical charge density cutoff and the regular grid generation method previously used for the computation of the electrostatic energy in firstprinciples simulations in the microcanonical or canonical ensembles. In particular, it is noted that a much higher cutoff is needed and that the most computationally efficient method of creating grids can result in poor simulations. Analysis of the simulation trajectories using a very large charge density cutoff at 1200 Ry and four different grid generation methods point to a substantially underestimated liquid density of about 0.85 g/cm{sup 3} resulting in a somewhat understructured liquid (with a value of about 2.7 for the height of the first peak in the oxygen/oxygen radial distribution function) for BLYP-GTH water at ambient conditions.

First-principles calculations can provide a powerful tool for investigating and optimizing electrode materials. While the strength of computations lies in the ability to control what is being calculated, the challenge is to ensure that the calculation is relevant for the physical processes that dominate the performance of the material. We will discuss this balance and show examples of how computations can aid in the design of current Li-ion rechargeable battery electrode materials by identifying and understanding the performance bottlenecks on the atomistic level. As the most commonly used anode in today's Li-ion batteries, graphite shows poor rate capability at lower temperatures, leading to over-potential and Li plating. Using first-principles calculations, coupled with a cluster expansion of Li interactions and kinetic Monte Carlo we were able to show that intrinsic Li diffusion in graphite can be very fast, providing guidance towards designing higher-rate carbonaceous anode materials. On the cathode side, we have studied the layered Li(Ni1/3,Mn1/3,Co1/3)O2 material, which is an interesting candidate if Co is partially substituted by the cheaper Al. Li migration in this material is influenced by several factors such as Li slab space, cation ordering and interlayer mixing. We present ab initio calculations of Li diffusivity as a function of Al content and slab spacing in the layered material, which elucidates the intrinsic rate performance effect of the Al substitution in the bulk material.

The large atomic-size mismatch between In and Ga and the large lattice-mismatch strain between InAs and GaAs make the InAs/GaAs (001) growth interface a complex alloy system, the understanding of which can enhance control of device synthesis and nanostructure self-assembly. We present a detailed first-principles analysis of the full progression of surface reconstructions observed on the InAs/GaAs(001) wetting layer during early stages of In deposition. We use systematic techniques to identify the most likely surface reconstruction prototypes of the InAs wetting layer on GaAs(001) using density functional theory (DFT) and then develop several cluster expansion Hamiltonians in order to thoroughly explore surface alloy disorder due to species substitution of In, Ga, and As at the surface. We use these results to construct a firstprinciples 0-K surface phase diagram of the InAs wetting layer on GaAs(001) and test the sensitivity of our predicted phase diagram to DFT approximations and convergence errors. We find two alloy configurations of the (4×3) structural prototype that are likely ground-state surface reconstructions, and simulated scanning tunneling micrographs (STM) of these reconstructions indicate that they can explain prominent features of experimentally obtained STM of the InAs/GaAs (4×3) surface.

We report a computationally tractable approach to first-principles investigation of time-dependent current of molecular devices under a steplike pulse. For molecular devices, all the resonant states below Fermi level contribute to the time-dependent current. Hence calculation beyond wideband limit must be carried out for a quantitative analysis of transient dynamics of molecules devices. Based on the exact nonequilibrium Green’s-function (NEGF) formalism of calculating the transient current [J. Maciejko, J. Wang, and H. Guo, Phys. Rev. B 74, 085324 (2006)10.1103/PhysRevB.74.085324], we develop two approximate schemes going beyond the wideband limit, they are all suitable for first-principles calculation using the NEGF combined with density-functional theory. Benchmark test has been done by comparing with the exact solution of a single level quantum dot system. Good agreement has been reached for two approximate schemes. As an application, we calculate the transient current using the first approximated formula with opposite voltage VL(t)=-VR(t) in two molecular structures: Al-C5-Al and Al-C60-Al . As illustrated in these examples, our formalism can be easily implemented for real molecular devices. Importantly, our new formula has captured the essential physics of dynamical properties of molecular devices and gives the correct steady state current at t=0 and t?? .

We present comparative analysis of microscopic mechanisms relevant to plastic deformation of the face-centered cubic (FCC) metals Al, Cu, and Ni, through determination of the temperature-dependent free energies of intrinsic and unstable stacking faults along [1 \\bar{1} 0] and [1 \\bar{2} 1] on the (1?1?1) plane using first-principles density-functional-theory-based calculations. We show that vibrational contribution results in significant decrease in the free energy of barriers and intrinsic stacking faults (ISFs) of Al, Cu, and Ni with temperature, confirming an important role of thermal fluctuations in the stability of stacking faults (SFs) and deformation at elevated temperatures. In contrast to Al and Ni, the vibrational spectrum of the unstable stacking fault (USF_{[1\\,\\bar{2}\\,1]}) in Cu reveals structural instabilities, indicating that the energy barrier (?usf) along the (1?1?1)[1 \\bar{2} 1] slip system in Cu, determined by typical first-principles calculations, is an overestimate, and its commonly used interpretation as the energy release rate needed for dislocation nucleation, as proposed by Rice (1992 J. Mech. Phys. Solids 40 239), should be taken with caution.

Ultrathin AlOx layers are nowadays widely employed to make tunneling junctions and, as a common practice, experimental transport data are often rationalized in terms of analytical models invoking effective electronic and geometric properties of the oxide layer. In this paper we examine the reliability of such models by performing first-principles simulations of the transport properties of Al/AlOx/Al junctions. The band gap, effective mass, and interface width obtained from ground state density-functional calculations are used within a potential barrier model, known also as the Simmons model, and its predictions of the conductance are compared with first-principles results. We also propose an analytical expression for the conductance based on a tight-binding model of the interface oxide. We show that the success of the potential barrier model in fitting experimental transport measurements rests on its formal similarity with the tight binding model which, in contrast to the former, is directly related to the realistic electronic structure of the interface.

Pure zircon and scheelite LuVO{sub 4} were prepared by solid state reaction and high-pressure route, respectively. Structure, elastic constants, lattice dynamics and thermodynamics of LuVO{sub 4} polymorphs were studied by experiments and firstprinciples calculation. Calculations here are in good agreement with the experimental results. The phonon dispersions of LuVO{sub 4} polymorphs were studied by the linear response method. The calculated phonon dispersions show that zircon and scheelite LuVO{sub 4} phases are dynamically stable. Raman-active frequencies were measured and assigned to different modes according to the calculations. The internal frequencies shift downward after phase transition from zircon to scheelite. Born effective charge tensors elements for both phases are analyzed. The finite temperature thermodynamic properties of LuVO{sub 4} polymorphs were calculated from the obtained phonon density of states by quasi-harmonic approach. - Graphical abstract: Lutetium orthovanadate polymorphs were synthesized by SSR and HP methods and their physical and chemical properties, including lattice dynamical properties, were determined by DFT calculations and experiments. Display Omitted - Highlights: • Pure zircon and scheelite LuVO{sub 4} polymorphs were synthesized by solid state reaction and high-pressure route. • Chemical and physical properties of LuVO4 polymorphs were studied by experiments and firstprinciples calculation. • Raman-active frequencies were measured and assigned to different modes according to the calculations. • Lattice dynamics of polymorphs were discussed in details.

Since its fabrication in 2004, graphene has attracted huge attention due to its exceptional electronic properties, and is now considered as one of the most promising candidates to replace the current semiconductor technology as silicon approaches its miniaturization limit. However, the absence of an electronic band gap in pristine graphene makes it ill-suited for many electronic applications. Semiconducting character can be imparted by a variety of methods, including chemical or structural modifications. For instance, a band gap can be opened by confining the electronic wave function in one dimension by cutting graphene to form graphene nanoribbons (GNRs). To possess a band gap comparable to conventional semiconductors like silicon, GNRs are required to have a width less than 3 nm and must also display sharp edges, which remains a great experimental challenge. Recently, a breakthrough advance has been achieved with the controlled synthesis of atomically precise nanoribbons using a bottom-up approach where small aromatic molecules chemically assemble into high-quality subnanometer ribbons. This method not only allows for the synthesis of high-quality straight GNRs, but also for more complex structures like wiggle-like GNRs, called graphene nanowiggles (GNWs). In Part I of this thesis, first-principles density functional theory (DFT) calculations are carried out on a variety of GNWs to reveal their unusual electronic and magnetic properties that are absent in their individual GNRs components, such as tunable band gaps and versatile magnetic states. The relationship between the band gap and the geometry is dictated by the armchair or zigzag characters of the corresponding parallel and oblique sectors, enabling GNWs to offer a broader set of geometrical parameters to tune the electronic structures compared to GNRs. In addition, first-principles many-body Green's function calculations within the GW approximation are performed to yield a quantitative prediction of GNWs' electronic properties. The enhanced electron-electron interaction in the quasi-one-dimensional GNWs results in significant self-energy corrections to their DFT band gaps. Consequently, the quasiparticle band gaps are typically more than twice of the DFT band gaps and are within the most interesting range 0.0-3.7 eV. In Part II of this thesis, we venture beyond graphene-based systems and investigate graphene-like materials: transition metal dichalcogenides MX 2(M = Mo, W; X = S). Similar to graphite, they are also layered structures stacked by weak van der Waals (vdW) forces. Single-layer MoS2 and WS2 have been synthesized and found to show enhanced carrier charge mobilities and strong photoluminescence with direct band gaps, and thus they have been considered as replacements or complements to graphene for applications. Raman spectroscopy is often considered as one of the most popular tools to characterize them. Despite extensive experimental Raman studies on MoS 2 and WS2, it remains unclear how Raman intensities and especially intensity ratio of Raman modes E2g1 and A1g depend on the materials' thickness, due to the large spectrum of seemingly contradictory findings. In the final part of the thesis (Part III), we highlight the experimental collaboration project with Prof. Plummer's group from Louisiana State University: spin-dependent surface reconstruction of layered Fe-based superconductors CaFe2As2. Low energy electron diffraction, scanning tunneling microscopy and spectroscopy, and first-principles spin-polarized DFT are utilized to investigate the geometric, electronic, and magnetic structures of the stripe-ordered (1x2) surface of Ca(Fe1-xCox) 2As2 (x=0, 0.075). The surface is terminated with a 50% Ca layer. Compared to the bulk, the surface Ca layer has a large inward relaxation (˜ 0.5 A), and the underneath As-Fe2-As layer displays a significant buckling. First-principles calculations show that the (1x2) phase is stabilized by the bulk anti-ferromagnetic spin ordering through the spin-charge-lattice coupling. Strikingly, a superconducting gap (˜7 meV

Firstprinciples calculations have been used to explore the Li–Bi–F ternary phase diagram. Our results confirm the thermodynamic stability of previously observed phases and find no new phases in this system. Electrochemical ...

We describe the analytical procedure for first-principles calibrations of 38Ar tracers in the U.S. Geological Survey (USGS) Laboratory in Menlo Park, California. The ages of fluence monitors determined in the USGS laboratory and those reported in the literature differ by nearly 2 percent. However, the radiogenic-40Ar content of the primary mineral standard on which these ages are based has never been verified by first-principles measurement in other laboratories.

“Realistic modeling” is a new direction of electronic structure calculations, where the main emphasis is made on the construction\\u000a of some effective low-energy model entirely within a first-principle framework. Ideally, it is a model in form, but with all\\u000a the parameters derived rigorously, on the basis of first-principles electronic structure calculations. The method is especially\\u000a suit for transition-metal oxides and

A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The ?GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b_{1} energy level in water. The application to the specific cases of nonpolar (101[over ¯]0) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and the dynamical fluctuations in the interface Zn-O and O-H bond orientations. These effects contribute up to 0.5 eV. PMID:25379929

The titanium adsorption on Si(100) is investigated using firstprinciples computer modelling methods. Two new subsurface adsorption sites are described. They are located at the edge of the cavity topped by a surface silicon dimer. The migration of the titanium from the surface to the subsurface sites is facilitated when occurring via one of these sites. The ejection of one of the silicon atoms forming the surface dimer is also investigated. The actual step of the ejection requires more energy than previously thought although, when considering the global picture of a titanium atom on the surface leading to the ejection of a silicon atom, the overall rate is compensated by the facilitated migration of the titanium to the subsurface sites. The consecutive adsorption of a second and third titanium atom is also investigated. It is shown that titanium grows evenly on the surface in normal condition, showing no intermixing of the titanium and silicon beyond the silicon layer.

A net-like nanostructure of silicon named silicon nanonet was designed and oxygen atoms were used to passivate the dangling bonds. First-principles calculation based on density functional theory with the generalized gradient approximation (GGA) were carried out to investigate the energy band gap structure of this special structure. The calculation results show that the indirect–direct band gap transition occurs when the nanonets are properly designed. This band gap transition is dominated by the passivation bonds, porosities as well as pore array distributions. It is also proved that Si–O–Si is an effective passivation bond which can change the band gap structure of the nanonets. These results provide another way to achieve a practical silicon-based light source. PMID:20596312

The crystal, electronic structural, elastic and the thermodynamic properties of LiNbO3 and LiTaO3 are investigated by using the first-principles plane-wave pseudopotential density function theory within the generalized gradient approximation (GGA) or local density approximation (LDA). The calculated equilibrium lattice parameters, elastic properties and the bulk modulus for LiNbO3 and LiTaO3 are in good agreement with the available experimental data. Furthermore, the static dielectric constant, optical permittivity and effective mass are reported. Finally, the thermodynamic properties of LiNbO3 and LiTaO3 such as the free energy, entropy, enthalpy, heat capacity and Debye temperature are given for reference.

The high-temperature phase transition between the tetragonal (scheelite) and monoclinic (fergusonite) forms of yttrium tantalite (YTaO4 ) has been studied using a combination of first-principles calculations and a Landau free-energy expansion. Calculations of the Gibbs free energies show that the monoclinic phase is stable at room temperature and transforms to the tetragonal phase at 1430 °C, close to the experimental value of 1426±7 °C. Analysis of the phonon modes as a function of temperature indicate that the transformation is driven by softening of transverse acoustic modes with symmetry Eu in the Brillouin zone center rather than the Raman-active Bg mode. Landau free-energy expansions demonstrate that the transition is second order and, based on the fitting to experimental and calculated lattice parameters, it is found that the transition is a proper rather than a pseudoproper type. Together these findings are consistent with the transition being ferroelastic.

We present first-principles calculations on the generalized-stacking-fault (GSF) energies and surface properties for several HCP metals on Mg, Be, Ti, Zn, and Zr, employing density functional theory (DFT) within generalized-gradient-approximation (GGA) and spin-polarized GGA (SGGA) using the Vienna ab initio simulation package (VASP). Using a supercell approach, stacking fault energies for the [1 1 2¯ 0] and [1 0 1¯ 0] slip systems, and surface properties on basal plane (0 0 0 1) have been determined. Our results show that GSF energy is sensitive to the primitive cell volumes and the ratio c/a for HCP metals. A spin-polarized calculations should be considered for transition-metal Ti, Zn, and Zr. The results for Mg from this work are good with ones from the previous ab initio and the experiments.

Here we introduce a new approach to compute the finite temperature lattice dynamics from firstprinciples via the newly developed slave mode expansion. We study PbTe where inelastic neutron scattering reveals strong signatures of nonlinearity as evidenced by anomalous features which emerge in the phonon spectra at finite temperature. Using our slave mode expansion in the classical limit, we compute the vibrational spectra and show remarkable agreement with temperature dependent inelastic neutron scattering measurements. Furthermore, we resolve an experimental controversy by showing that there are no appreciable local nor global spontaneously broken symmetries at finite temperature and that the anomalous spectral features simply arise from two anharmonic interactions. Our approach should be broadly applicable across the periodic table. PMID:25238367

The electronic, vibrational, and superconducting properties of LiBe alloy in the P2 1/m structure under pressure have been investigated using first-principles calculations. The calculated electron-phonon coupling (EPC) of LiBe with both linear response theory and the rigid muffin-tin approximation suggested that pairing electrons are mainly mediated by the Li low-lying phonon vibrations, and the increase of the Li EPC matrix element with pressure is responsible for the increased EPC parameter ?. The application of the Allen-Dynes modified McMillan equation reveals high superconducting critical temperatures of 15.2 K at 80 GPa and 18.4 K at 100 GPa for P2 1/m LiBe.

Applying the first-principles with the generalized gradient approximation and the modified Becke and Johnson potential plus the generalized gradient approximation potential as exchange correlation potential, the electronic structures, half-metallicity and the cohesive energy for hypothetical zinc blende YC compound are calculated. Obtained results show that the zinc blende YC is typical half-metallic with a large half-metallic gap of 0.67(2) eV and magnetic moment of 1.00 ?B per molecule. Magnetic moments mainly come from the p orbital of C atom, where p-d hybridization mechanism plays a dominating role in the formation of half-metallicity. The relatively stable ferromagnetic ground state, large half-metallic gap, the robust half-metallicity with respect to the lattice constant compression, and negative cohesive energy indicate zinc blende YC would be a promising half metallic ferromagnet.

A series of point defects in uranium mononitride (UN) have been studied by first-principles DFT+U calculations. The influence of intrinsic defects on the properties of UN was explored by considering the anti-ferromagnetic (AFM) order along the [001] direction. Our results show that all the point defects lead to obvious volume swelling of UN crystal. Energetically, the interstitial nitrogen defect is the most favorable one among single-point defects in UN crystal with the formation energy of 4.539 eV, while the N-Frenkel pair becomes the most preferable one among double-point defects. The AFM order induces obvious electron spin polarization of uranium towards neighboring uranium atoms with opposite spin orientations in UN crystal.

Structural and bonding patterns arising from the incorporation of fluorine atoms in a graphene-like network relevant to the deposition of carbon fluoride (CF x) films were addressed by first-principles calculations. We find that large N-member ( N = 8-12) rings, defects by sheet branching, and defects associated with bond rotation pertain to CF x. The cohesive energy gains associated with these patterns are ˜0.2-0.4 eV/at., which is similar to those for a wide range of defects in other C-based nanostructured solids. Fullerene-like CF x is predicted for F concentrations below ˜10 at.%, while CF x compounds with higher F content are predominantly amorphous or polymeric.

We present a newly developed publicly available genetic algorithm (GA) for global structure optimisation within atomic scale modeling. The GA is focused on optimizations using firstprinciples calculations, but it works equally well with empirical potentials. The implementation is described and benchmarked through a detailed statistical analysis employing averages across many independent runs of the GA. This analysis focuses on the practical use of GA's with a description of optimal parameters to use. New results for the adsorption of M8 clusters (M = Ru, Rh, Pd, Ag, Pt, Au) on the stoichiometric rutile TiO2(110) surface are presented showing the power of automated structure prediction and highlighting the diversity of metal cluster geometries at the atomic scale.

Using first-principles calculations, we have systematically investigated the magnetic properties of Mg-doped AlN [Formula: see text] and [Formula: see text] surfaces. Both the polar and non-polar surfaces are found to be magnetic and the magnetic moments are mainly due to spin polarized 2p orbitals of surface N atoms surrounding Mg. The splitting of energy levels in both cases favours charge hopping between the minority spin states of N 2p orbitals, which leads to a stable ferromagnetic ground state. However, the range of magnetic coupling and the stability of the ferromagnetic state differ between the polar and non-polar surfaces and are dependent on the nature of localization of the defect states. The ferromagnetic state in a Mg-doped reconstructed [Formula: see text] surface is more stable than in a Mg-doped AlN [Formula: see text] surface. PMID:25299568

The dielectric function and second-harmonic generation spectrum of ferroelectric LiNbO(3) are calculated from firstprinciples. The calculations are based on the electronic structure obtained within density functional theory. The use of the GW approach to account for quasiparticle effects and the subsequent solution of the Bethe-Salpeter equation lead to a dielectric function in excellent agreement with measured data. The second harmonic generation spectrum calculated within the independent (quasi) particle approximation predicts strong nonlinear coefficients for photon energies above about 1.5 eV. The comparison with measured data suggests that the inclusion of self-energy effects in the nonlinear response improves the agreement with experiment. PMID:23007763

perform first-principles calculations to investigate liquid iron-sulfur alloys (Fe, Fe56S8, Fe52S12, and Fe48S16) under high-pressure and high-temperature (150-300 GPa and 4000-6000 K) conditions corresponding to the Earth's outer core. Considering only the density profile, the best match with the preliminary reference Earth model is by liquid Fe-14 wt % S (Fe50S14), assuming sulfur is the only light element. However, its bulk sound velocity is too high, in particular in the deep outer core, suggesting that another light component such as oxygen is required. An experimental check using inelastic X-ray scattering shows good agreement with the calculations. In addition, a present study demonstrates that the Birch's law does not hold for liquid iron-sulfur alloy, consistent with a previous report on pure liquid iron.

Through first-principles computations, we investigated Li4NiTeO6, which is a new layered Ni-based cathode material for Li ion batteries, by focusing on the sequence of Li removal when it is charged. According to our computations, Li4NiTeO6 exhibits satisfactory structural stability with a volume change of 7.2% and electrical conductivity similar to Li2MnO3. We also examined the electronic configuration of this cathode material during its electrochemical progress and found a weak hybridization of Ni3d and O2p. Moreover, by analyzing the Bader charges of different elements, we confirmed that O and Ni are exclusively responsible for electron loss and gain. In addition, O evolution reactions occur when half of Li(+) ions are extracted. Finally, we investigated Li(+) migration paths and concluded that migration barriers depend on the charge distribution around migration paths. PMID:24967833

The ferroelectric mechanism of croconic acid in terms of the electronic structure and the molecular structure was studied by firstprinciples using the density functional theory with the generalized gradient approximation. The spontaneous polarization (Ps) was simulated by the Berry phase method. It is found that the large polarization originates from charge transfer due to the strong "push-pull" effect of electron-releasing and -withdrawing groups along the hydrogen bond. According to the characteristics of polarization of croconic acid, we constructed a one-dimensional ferroelectric Hamiltonian model to describe the ferroelectric properties of croconic acid. Based on the Hamiltonian model, the thermal properties of the ferroelectricity of croconic acid were studied by Monte Carlo method. The simulated Curie temperature is 756 K, and the spontaneous polarization keeps well temperature range stability up to 400 K. These results are in good agreement with the experimental data. PMID:23901998

We report a first-principles prediction of the Raman shifts of parahydrogen (pH2) clusters of sizes N = 4-19 and 33, based on path integral ground-state simulations with an ab initio potential energy surface. The Raman shifts are calculated, using perturbation theory, as the average of the difference-potential energy surface between the potential energy surfaces for vibrationally excited and ground-state parahydrogen monomers. The radial distribution of the clusters is used as a weight function in this average. Very good overall agreement with experiment [G. Tejeda, J. M. Fernández, S. Montero, D. Blume, and J. P. Toennies, Phys. Rev. Lett. 92, 223401 (2004)] is achieved for p(H2)2-8,13,33. A number of different pair potentials are employed for the calculation of the radial distribution functions. We find that the Raman shifts are sensitive to slight variations in the radial distribution functions.

A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b1 energy level in water. The application to the specific cases of nonpolar (101 ¯0) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and the dynamical fluctuations in the interface Zn-O and O-H bond orientations. These effects contribute up to 0.5 eV.

CuIn2 is not found in the standard phase diagram of the Cu-In system. However CuIn2 formation was observed at the interface between Cu and In films after isothermal treatment was applied.( W. Keppner, T. Klas, W. Körner, R. Wesche and G. Schatz, Phys. Rev. Lett. 49), 1735 (1982). Experimentally the Cu-In interface structure was determined by x-ray diffraction as CuIn_2, structurally equivalent with CuAl2 and AgIn_2. We used Density Functional Theory in the Local Density Approximation to perform firstprinciples total energy calculations of CuIn2 in the experimental and related structures using a full-potential LAPW method. We discuss its heat of formation, phase-stability and bulk properties.

We report first-principles studies on systems formed by alkali metal (Na, K, or Rb) added to zeolite ITQ-4. Geometric and electronic structures of the quasi-1D chains of intercalated alkali metal atoms at experimental loading (4 metal atoms per 32 Si) are studied. Clear differences between different kinds of alkali metal are found, with a general trend of decreased ionization and less metallic character for the lighter alkali metals. Within the zeolite channels, it is possible to form insulated and metallic alkali metal chains by doping Na or Rb. Agreeing with experiments, only Rb here is found to be a good candidate to generate inorganic electride. We also predict that a large quantity of Na can be doped into the zeolite channel, while no more than 4 Rb per 16 Si can be doped.

Firstprinciples study of electronic and mechanical properties of ternary phase Zr2TiAl intermetallic compound has been carried out by using full potential linear augmented plane wave (FP-LAPW) method. Our calculated lattice parameter is in good agreement with the experiment. We find the magnetic phase of the compound to be stable with a magnetic moment of 1.95 ?B. The major contribution to the total magnetic moment arises mainly from the Ti atom with the local magnetic moment of 1.22 ?B. From the density of states plots we find the Ti-d and Zr-d to dominate at the Fermi level (EF) with enhanced crystal field splitting and exchange splitting found in Ti. The mechanical stability of the compound is confirmed from the calculated elastic constants, and we find the compound to be ductile in nature from the calculated Pugh's ratio and Cauchy's pressure.

We utilized first-principles density-functional-theory (DFT) calculations to evaluate the thermodynamic feasibility of a pyroprocessing methodology for reducing the volume of high-level radioactive materials and recycling spent nuclear fuels. The thermodynamic properties of transuranium elements (Pu, Np and Cm) were obtained in electrochemical equilibrium with a LiCl-KCl molten salt as ionic phases and as adsorbates on a W(110) surface. To accomplish the goal, we rigorously calculated the double layer interface structures on an atomic resolution, on the thermodynamically most stable configurations on W(110) surfaces and the chemical activities of the transuranium elements for various coverages of those elements. Our results indicated that the electrodeposition process was very sensitive to the atomic level structures of Cl ions at the double-layer interface. Our studies are easily expandable to general electrochemical applications involving strong redox reactions of transition metals in non-aqueous solutions.

Hydrogen reactions with silicon substrates is an established technique for the study and control of surface morphology. Here, we report the results of first-principles calculations on the trapping and depassivation reactions involving excess hydrogen (x-H) at a fully H-passivated Si(111) surface. We find that x-H atoms can depassivate Si-H bonds with a small barrier of 0.8eV , or they can get trapped in very stable configurations that comprise of a dihydride and a vicinal Si-H bond. Desorption of H2 molecules from these complexes has an activation energy of 1.68eV , which can account for pertinent experimental data. We discuss also the effect of strain on the possibility of altering the x-H surface profile.

The effect of strain on the electronic properties of BC3 sheet was studied by using first-principles density functional theory. It is found that the band gap of BC3 sheet increases gradually when the applied tensile strain ranges from 0% to 12.5%. While the band gap decreases as the compressive strain is applied, especially resulting in the semiconductor-metal transition at some strain. Further analysis shows that the change of band gap mainly results from the variation of the energy of valence band maximum (VBM), which is related to the strength of the bonding state. The proposed mechanical control of the electronic properties will widen the application of BC3 sheet in future nanotechnology.

We have performed density functional theory-based first-principles calculations to study the stability, geometrical structures, and electronic/magnetic properties of pure graphene, sodium (Na)-adsorbed graphene and also the adsorption properties of H_2 -molecular ranging from one to five molecules on their preferred structures. Using the information of binding energy of Na at different adsorption sites of varying sized graphene supercell, it has been observed that hollow position is the most preferred site for Na adsorption, and the same in 3 × 3 supercell has been used for further calculations. The band structure and density of states calculations have been performed to study the electronic/magnetic properties of Na-atom graphene. On comparing adsorption energy per H_2 -molecular in pure and Na-adsorbed graphene, we find that presence of Na atom, in general, enhances binding strength to H_2 -moleculars.

Fading is the time-dependent variation in transmitted signal strength through a complex medium due to interference or temporally evolving multipath scattering. In this paper we use random matrix theory (RMT) to establish a first-principles model for fading, including both universal and nonuniversal effects. This model provides a more general understanding of the most common statistical models (Rayleigh fading and Rice fading) and provides a detailed physical basis for their parameters. We also report experimental tests on two ray-chaotic microwave cavities. The results show that our RMT model agrees with the Rayleigh and Rice models in the high-loss regime, but there are strong deviations in low-loss systems where the RMT approach describes the data well.

Intriguing electronic and magnetic properties of BN layer with noble metal (Pd, Pt, Ag and Au) doping are obtained by first-principles calculations. Adsorbed Pd (or Pt) reduces the band gap of BN sheet owing to the induction of impurity states. The unpaired electrons in the Ag (or Au)-adsorbed and the Pd (or Pt)-substituted BN layers are polarized, and thus exhibit a magnetic moment of 1.0 µB, leading to these BN configurations to be magnetic semiconductors. The half-metallic feature of the Ag-substituted BN layer, along with the delocalization of spin states, renders this configuration an excellent spin filter material. Thus, these findings offer a unique opportunity for developing BN-based nanoscale devices.

The structural and electronic properties of undoped and Ag-doped unpassivated wurtzite GaAs nanowires (NWs), as well as their stability, are investigated within the first-principles frame. The calculated formation energies show that the single Ag energetically prefers to substitute the surface Ga (Ef = -0.529 eV) under As-rich conditions, and creates a much shallower (0.19 eV above the Fermi) acceptor level, which is of typical p-type character. With the increase in the Ag concentration, the p-type behavior gradually weakens and the n-type character arises. Thus, one can expect to synthesize Ag-doped GaAs NWs for p-type or n-type applications by controlling their Ag concentration and microarrangement.

The elastic and structural properties of Zr3Al3C5 have been investigated by means of first-principles pseudopotential total energy method. The lattice constants and internal parameters of atoms are in agreement with the available results. The pressure dependence with the elastic constants indicates Zr3Al3C5 possesses mechanical stability in the pressure range 0-40 GPa. The calculated Cauchy pressure and ratio of bulk modulus to shear modulus reveal that Zr3Al3C5 is intrinsically brittle in nature at zero pressure. Moreover, we derived the bulk and shear moduli, Young's moduli and Poisson's ratio from elastic constants for Zr3Al3C5. The variations of Debye temperature with pressure were estimated from the pressure dependence with average sound velocity.

We present a first-principles study on the spin dependent conductance of five single-atom magnetic junctions consisting of a magnetic tip and an adatom adsorbed on a magnetic surface, i.e., the Co-Co/Co(001) and Ni-X/Ni(001) (X = Fe, Co, Ni, Cu) junctions. When their spin configuration changes from ferromagnetism to anti-ferromagnetism, the spin-up conductance increases while the spin-down one decreases. For the junctions with a magnetic adatom, there is nearly no spin valve effect as the decreased spin-down conductance counteracts the increased spin-up one. For the junction with a nonmagnetic adatom (Ni-Cu/Ni(001)), a spin valve effect is obtained with a variation of 22% in the total conductance. In addition, the change in spin configuration enhances the spin filter effect for the Ni-Fe/Ni(001) junction but suppresses it for the other junctions.

First-principles fully relaxed tensile and shear test simulations were performed on \\Sigma 10(11\\bar {2}4)/[1\\bar {1}00] tilt Mg grain boundary (GB) models, with and without H segregation, to investigate mechanisms of H embrittlement of Mg. Strengthening as a result of covalent-like characteristics of Mg-H bonds prevailed over weakening of Mg-Mg bonds resulting from charge transfer; as a result, an H atom strengthened the GB. In addition, because the strong Mg-H bonds suppressed macroscopic GB fracture, elongation to failure was not reduced by H segregation. However, the resistance to GB shearing was increased by H segregation. It is therefore suggested that H segregation enhances crack growth at the GB, because dislocation emission from the crack tip is suppressed, resulting in H embrittlement of Mg.

We compute the bulk photovoltaic effect (BPVE) in BiFeO(3) using first-principles shift current theory, finding good agreement with experimental results. Furthermore, we reconcile apparently contradictory observations: by examining the contributions of all photovoltaic response tensor components and accounting for the geometry and ferroelectric domain structure of the experimental system, we explain the apparent lack of BPVE response in striped polydomain samples that is at odds with the significant response observed in monodomain samples. We reveal that the domain-wall-driven response in striped polydomain samples is partially mitigated by the BPVE, suggesting that enhanced efficiency could be obtained in materials with cooperative rather than antagonistic interaction between the two mechanisms. PMID:23368233

A first-principles-based effective Hamiltonian is used to investigate the thickness dependency of the size of straight-walled domains in ultrathin films made of the multiferroic BiFeO? (BFO) material. It is found that the Kittel law is followed, as in ferroelectric or ferromagnetic films. However, an original real-space decomposition of the different energetic terms of this effective Hamiltonian allows the discovery that the microscopic origins of such a law in BFO films dramatically differ from those in ferroelectric or ferromagnetic films. In particular, interactions between tilting of oxygen octahedra around the domain walls and magnetoelectric couplings near the surface (and away from the domain walls) play an important role in the observance of the Kittel law in the studied BFO films. PMID:21230868

We have performed a systematic first-principles investigation to calculate the electronic structures, mechanical properties, and phonon-dispersion curves of NpO2 . The local-density approximation+U and the generalized gradient approximation+U formalisms have been used to account for the strong on-site Coulomb repulsion among the localized Np5f electrons. By choosing the Hubbard U parameter around 4 eV, the orbital occupancy characters of Np5f and O2p are in good agreement with recent experiments [A. Seibert, T. Gouder, and F. Huber, J. Nucl. Mater. 389, 470 (2009)]. Comparing to our previous study of ThO2 , we note that stronger covalency exists in NpO2 due to the more localization behavior of 5f electrons of Np in line with the localization-delocalization trend exhibited by the actinides series.

We determine electronic structure and dielectric response of 25 and 50% Ti-substituted thoria (ThO2), using first-principles density functional theory calculations based on pseudopotentials and a plane wave basis. We find that Th0.75Ti0.25O2 is more promising as a high-k material than Th0.5Ti0.5O2. We show that the IR-active phonon modes in pure thoria can be tuned upon Ti doping and the softened modes cause an enhanced dielectric response of 25% Ti-doped thoria. As the material remains insulating, it holds promise for applications such as a gate oxide material.

Solid solutions formed by doping ThO2 with oxides of trivalent cations, such as Y2O3 and La2O3, are suitable for solid electrolyte applications, similar to doped zirconia and ceria. ThO2 has also been gaining much attention as an alternative to UO2 in nuclear energy applications, the aforementioned trivalent cations being important fission products. In both cases the mixing energetics and short-range ordering/clustering are key to understanding structural and transport properties. Using first-principles atomistic calculations, we address intra- and intersublattice interactions for both cation and anion sublattices in ThO2-based fluorite-type solid solutions and compare the results with similar modeling studies for related trivalent-doped zirconia systems.

Raman spectra of amorphous carbon nitride films (a-C:N) resemble those of typical amorphous carbon (a-C), and no specific features in the spectra are shown due to N doping. The present work provides a correlation between the microstructure and vibrational properties of a-C:N films from firstprinciples. The six periodic model structures of 64 atoms with various mass densities and nitrogen contents are generated by the liquid-quench method using Car—Parinello molecular dynamics. By using Raman coupling tensors calculated with the finite electric field method, Raman spectra are obtained. The calculated results show that the vibrations of C=N could directly contribute to the Raman spectrum. The similarity of the Raman line shapes of N-doped and N-free amorphous carbons is due to the overlapping of C=N and C=C vibration bands. In addition, the origin of characteristic Raman peaks is also given.

We describe the applications of first-principles calculations to the analysis of transport and magnetic properties of rare-earth materials. The first application is a detailed calculation of the spin-disorder resistivity of heavy rare-earth metals in the Gd-Tm series. The crystallographic anisotropy of the spin-disorder resistivity agrees well with experiment, but its magnitude is significantly underestimated. Possible origins of this discrepancy are discussed. In the second part we analyze the exchange interaction in Gd-doped EuO using a magnetostructural cluster expansion based on the ab initio total energies. The calculated Curie temperature has a broad maximum extending over 10-20% Gd concentration and reaching approximately 150 K.

An efficient method of calculating the natural bond orbitals (NBOs) based on a truncation of the entire density matrix of a whole system is presented for large-scale density functional theory calculations. The method recovers an orbital picture for O(N) electronic structure methods which directly evaluate the density matrix without using Kohn-Sham orbitals, thus enabling quantitative analysis of chemical reactions in large-scale systems in the language of localized Lewis-type chemical bonds. With the density matrix calculated by either an exact diagonalization or O(N) method, the computational cost is O(1) for the calculation of NBOs associated with a local region where a chemical reaction takes place. As an illustration of the method, we demonstrate how an electronic structure in a local region of interest can be analyzed by NBOs in a large-scale first-principles molecular dynamics simulation for a liquid electrolyte bulk model (propylene carbonate + LiBF4).

We have used firstprinciples methods to calculate the partitioning of water between perovskite and ringwoodite under lower mantle and Fe-free conditions. We find that incorporation of water into ringwoodite is more favourable than into perovskite by about 0.25 eV per formula unit, or about 24 kJ/mol. This translates to a ringwoodite to perovskite partition coefficient of between 10 and 13, depending on temperature. These values are in good agreement with the partitioning experiments of Inoue et al. (2010) on Fe-bearing samples, where they find a partition coefficient of about 15. We also find that water incorporates into perovskite more readily than into periclase (also under Fe-free conditions), and we predict a perovskite to periclase partition coefficient of 90 at 24 GPa and 1500 K. We conclude, therefore, that the lower-mantle is able to contain substantial amounts of water, perhaps as much as 1000 ppm.

We present a first-principles study of the magnetic properties of N-doped MgO, CaO and SrO, which have been proposed to constitute a new class of dilute magnetic semiconductors (DMSs) with no magnetic elements. In this study, it was found that under a homogeneously distributed condition, Curie temperatures could reach room temperature at sufficient N concentrations in the range of 20-30 at.%; however, an inhomogeneous N distribution in these DMSs is the favored configuration, which indicates that spinodal decomposition leads to a room-temperature blocking temperature at smaller N concentrations than those estimated for room-temperature ferromagnetism in the homogeneous distribution condition.

Ab initio Quantum mechanics calculations of the equation of states for BaZrO{sub 3} have been performed and the bulk modulus has been obtained. The value of the modulus is in good agreement with reported experimental values. Equilibrium proton positions in Y-doped BaZrO{sub 3} with dopant concentrations from 12.5 to 50% were investigated. Initial rough estimates of the transition barriers have been made. Our results suggest that the proton migration pathway may involve secondary minima with two maxima (symmetric with respect to the center of the path). In the next phase of this project the results of our quantum mechanical calculations will be used to develop a new Reactive Force Field (ReaxFF) based on firstprinciples. This Reactive Force Field will be used for much molecular dynamics simulations or much larger systems to investigate proton migration in bulk and surface regions of fuel cells.

The photochemical conversion of CO2 and H2O into energy-bearing hydrocarbon fuels provides an attractive way of mitigating the green-house gas CO2 and utilizing solar energy as a sustainable energy source. However, due to the high reduction potential and chemical inertness of CO2 molecules, the conversion rate of CO2 is impractically low. The activation of CO2 is critical in facilitating further reactions. By carrying out first-principles calculations of reaction pathways from CO2 to CO2^- anions on Ti-based oxides including zeolites in the presence of photoexcited electrons, we have studied the initial step of CO2 activation via 1e transfer. It is shown that the CO2 reactivity of these surfaces strongly depends on the crystal structure, surface orientation, and presence of defects. This opens a new dimension in surface structure modification to enhance the CO2 adsorption and reduction on semiconductor surfaces.

To give insight on developing Rh-based superalloys, systematic investigations on mechanical and electronic properties of fcc Rh and L12 Rh3Zr are conducted by first-principles calculation. Basic mechanical parameters including bulk modulus, elastic constants, shear modulus, Young's modulus, Poisson's ratio, and elastic anisotropy are calculated. Additionally, the ideal strengths are investigated under tensile and shear loading. Our results reveal that L12 Rh3Zr has lower mechanical strength but higher ductility than fcc Rh. The analysis of density of states reveals that the Rh-d electrons in L12 Rh3Zr become more localized, whereas the Zr-d electrons become more delocalized, than in pure bulk, due to the interaction of Rh and Zr.

In this work, firstprinciples calculation of structural, electronic and elastic properties of thorium monopnictides ThX (N, P, As, Sb and Bi) are presented. The calculations are performed by a developed full-potential augmented plane wave plus local orbitals (FP-L/APW+lo) method within the density functional theory (DFT). The exchange and correlation potential energies are treated according to the generalized gradient approximation (GGA) using the Perdew, Burke, Ernzerhof (PBE) parameterization, and the local density approximation (LDA). We have calculated the lattice parameters, bulk modulii and the first pressure derivatives of the bulk modulii. The elastic properties of the studied compounds are only investigated in the most stable calculated phase. We have obtained Young's modulus, shear modulus, Poisson's ratio, anisotropy factor and Kleinman parameter by the aid of the calculated elastic constants. We discuss the total and partial densities of states and charge densities.

We performed first-principles molecular dynamics calculations at finite temperature, to study the interacting conformations of Lewis-X (LeX) trisaccharides in the crystalline phase. The calculated cell parameters and detailed atomic structure of the LeX molecule compare well to the experimental data obtained by X-ray diffraction. We identify and characterize the hydrogen-bond network, responsible for the mutual interaction of the LeX pairs, whereas we find the intramolecular conformation and stability to be mainly assured by dispersion forces. The relative contributions to the crystallization energy of the hydrogen bonds and of the dispersion forces are defined and quantified. From this study, candidate configurations for the fully hydrated, in vivo structures of homotypic LeX-LeX interactions at cell surfaces can be proposed. We discuss how these configurations could also be relevant for the adhesion and self-assembly of nanostructures. PMID:21919496

The electronic structure and formation energies of N-doped CuAlO2 are studied using first-principles calculations. It is found that, when a N atom is doped into CuAlO2, the N atom prefers to substitute an O atom rather than to occupy an interstitial site of the Cu layer. The NO acts as a shallow accepter while the Ni acts as a deep accepter. The results of the electronic structure show that the N-doping doesn't alter the band gap of CuAlO2 for the both cases. In the substitutional case, the N impurity states occur at the top of valance band maximum (VBM), which provides holes and increases the p-type conductivity. However, in the interstitial case, the N impurity states occur in the middle of the band gap, which are more localized and this indicates that it is not good for p-type conductivity.

Mercury dichloride is an ionic compound solidifying into a unique layer structure of rod-like monomers, so that unusual structural and physical properties can be expected for its liquid state. We propose a set of pseudoclassical interionic potentials, including three-body forces and electronic-polarization terms, patterned on the results of relativistic first-principles calculations on the molecular monomer, dimer and trimer. The proposed force law will allow structural studies of the condensed phases by molecular-dynamics simulations, with the main aims of exploring the nature of the short-range and intermediate-range order in the melt and the process of ionization at high pressure and temperature.

Geomagnetically induced currents (GIC) during space storms pose a risk to power transmission grids across the globe. As part of the European Risk from Geomagnetically Induced Currents (EURISGIC) EU/FP7 project the Finnish Meteorological Institute is developing a firstprinciples based GIC forecasting and warning system. The system is given as input the solar wind plasma parameters measured by the ACE spacecraft and the final output consists of the ground electric field and GIC in a simplified model of European high-voltage power grids. We describe the different steps involved in obtaining the final GIC solution and implementation of the required software components. We also present a comparison between simulated electrojet indicators and those derived from the magnetic field measurements of the IMAGE magnetometer network. Additionally the simulated GIC are compared to natural gas pipeline observations in Mäntsälä, Finland.

The fundamental equation governing a non-relativistic quantum system of N particles is the time-dependant Schroedinger Equation [Schroedinger, 1926]. In 1965, Kohn and Sham proposed to replace this original many-body problem by an auxiliary independent-particles problem that can be solved more easily (Density Functional Theory). Solving this simplified problem requires to find the subspace of dimension N spanned by the N eigenfunctions {Psi}{sub i} corresponding to the N lowest eigenvalues {var_epsilon}{sub i} of a non-linear Hamiltonian operator {cflx H} determined from first-principles. From the solution of the Kohn-Sham equations, forces acting on atoms can be derived to optimize geometries and simulate finite temperature phenomenon by molecular dynamics. This technique is used at LLNL to determine the Equation of State of various materials, and to study biomolecules and nanomaterials.

We present first-principles calculations of the thermal and thermal transport properties of Bi2Te3 that combine an ab initio molecular dynamics (AIMD) approach to calculate interatomic force constants (IFCs) along with a full iterative solution of the Peierls-Boltzmann transport equation for phonons. The newly developed AIMD approach allows determination of harmonic and anharmonic interatomic forces at each temperature, which is particularly appropriate for highly anharmonic materials such as Bi2Te3. The calculated phonon dispersions, heat capacity, and thermal expansion coefficient are found to be in good agreement with measured data. The lattice thermal conductivity, ?l, calculated using the AIMD approach nicely matches measured values, showing better agreement than the ?l obtained using temperature-independent IFCs. A significant contribution to ?l from optic phonon modes is found. Already at room temperature, the phonon line shapes show a notable broadening and onset of satellite peaks reflecting the underlying strong anharmonicity.

Using first-principles density functional theory, we show that, in Mn(2)NiSn, an energy lowering phase transition from the cubic to tetragonal phase occurs which indicates a martensitic phase transition. This structural phase transition is nearly volume-conserving, implying that this alloy can exhibit shape memory behavior. The magnetic ground state is a ferrimagnetic one with antiparallel Mn spin moments. The calculated moments with different electronic structure methods in the cubic phase compare well with each other but differ from the experimental values by more than 1 ?(B). The reason behind this discrepancy is explored by considering antisite disorder in our calculations, which indicates that the site ordering in this alloy can be quite complex. PMID:21540519

The absent critical thickness of fully relaxed asymmetric ferroelectric tunnel junctions is investigated by first-principles calculations. The results show that PbTiO{sub 3} thin film between Pt and SrRuO{sub 3} electrodes can still retain a significant and stable polarization down to thicknesses as small as 0.8 nm, quite unlike the case of symmetric ferroelectric tunnel junctions. We trace this surprising result to the generation of a large electric field by the charge transfer between the electrodes caused by their different electronic environments, which acts against the depolarization field and enhances the ferroelectricity, leading to the reduction, or even complete elimination, for the critical thickness.

We have calculated the thermal conductivities (?) of cubic III-V boron compounds using a predictive firstprinciples approach. Boron arsenide is found to have a remarkable room temperature ? over 2000 W m(-1) K(-1); this is comparable to those in diamond and graphite, which are the highest bulk values known. We trace this behavior in boron arsenide to an interplay of certain basic vibrational properties that lie outside of the conventional guidelines in searching for high ? materials, and to relatively weak phonon-isotope scattering. We also find that cubic boron nitride and boron antimonide will have high ? with isotopic purification. This work provides new insight into the nature of thermal transport at a quantitative level and predicts a new ultrahigh ? material of potential interest for passive cooling applications. PMID:23889420

We have calculated the thermal conductivities (?) of cubic III-V boron compounds using a predictive firstprinciples approach. Boron arsenide is found to have a remarkable room temperature ? over 2000Wm-1K-1; this is comparable to those in diamond and graphite, which are the highest bulk values known. We trace this behavior in boron arsenide to an interplay of certain basic vibrational properties that lie outside of the conventional guidelines in searching for high ? materials, and to relatively weak phonon-isotope scattering. We also find that cubic boron nitride and boron antimonide will have high ? with isotopic purification. This work provides new insight into the nature of thermal transport at a quantitative level and predicts a new ultrahigh ? material of potential interest for passive cooling applications.

New structures of body-centered, tetragonal C4 carbon allotropes containing a mixture of sp (triple yne bond) and sp3 (single bond) hybridization were designed using first-principles calculations. These three structures named 1-Yne, 2-Yne and 3-Yne C4 carbon not only maintained the tetragonal space group (SG# 139) of C4 carbon, but also exhibited unique physical and chemical properties due to triple-like bonding. The dynamic stability of these structures was confirmed using phonon calculations, and the entire structure showed a unique phonon spectrum with an Eigen-frequency of ~2250 cm-1, which is a characteristic of a triple bond. Structure prediction by X-ray simulations was performed and the band structure due to triple bond modification was identified. Details of the bulk properties, such as lattice constant, bond length and bulk modulus, could be explained well by a simple physical picture due to the triple bond.

First-principles calculations with van der Waals correction included are carried out to investigate the intercalation and diffusion of molecular hydrogen in single-layer and bulk graphdiyne, which is crucial for understanding and improving the hydrogen storage capacity of graphdiyne. Different intercalation sites and hydrogen molecular orientations have been considered and compared. It is found that configurations with the axis of the hydrogen molecule parallel to graphdiyne layers are favoured. In contrast to graphite where hydrogen diffusion is restricted within the interlayer space, the unique porous structure of graphdiyne enables three-dimensional diffusion of hydrogen (in-plane diffusion and out-plane diffusion) with moderate energy barriers, thus ensuring easy hydrogen loading and unloading. The in-plane diffusion barriers largely depend on the interlayer distance, whereas the interlayer spacing has little effect on the out-plane diffusion barriers. This experimentally available novel carbon allotrope is expected to find applications in hydrogen storage.

Here we introduce a new approach to compute the finite temperature lattice dynamics from firstprinciples via the newly developed slave mode expansion. We study PbTe where inelastic neutron scattering reveals strong signatures of nonlinearity as evidenced by anomalous features which emerge in the phonon spectra at finite temperature. Using our slave mode expansion in the classical limit, we compute the vibrational spectra and show remarkable agreement with temperature dependent inelastic neutron scattering measurements. Furthermore, we resolve an experimental controversy by showing that there are no appreciable local nor global spontaneously broken symmetries at finite temperature and that the anomalous spectral features simply arise from two anharmonic interactions. Our approach should be broadly applicable across the periodic table.

The high substrate specificity of fluoroacetate dehalogenase was explored by using crystallographic analysis, fluorescence spectroscopy, and theoretical computations. A crystal structure for the Asp104Ala mutant of the enzyme from Burkholderia sp. FA1 complexed with fluoroacetate was determined at 1.2 Å resolution. The orientation and conformation of bound fluoroacetate is different from those in the crystal structure of the corresponding Asp110Asn mutant of the enzyme from Rhodopseudomonas palustris CGA009 reported recently (J. Am. Chem. Soc. 2011, 133, 7461). The fluorescence of the tryptophan residues of the wild-type and Trp150Phe mutant enzymes from Burkholderia sp. FA1 incubated with fluoroacetate and chloroacetate was measured to gain information on the environment of the tryptophan residues. The environments of the tryptophan residues were found to be different between the fluoroacetate- and chloroacetate-bound enzymes; this would come from different binding modes of these two substrates in the active site. Docking simulations and QM/MM optimizations were performed to predict favorable conformations and orientations of the substrates. The F atom of the substrate is oriented toward Arg108 in the most stable enzyme-fluoroacetate complex. This is a stable but unreactive conformation, in which the small O-C-F angle is not suitable for the S(N)2 displacement of the F(-) ion. The cleavage of the C-F bond is initiated by the conformational change of the substrate to a near attack conformation (NAC) in the active site. The second lowest energy conformation is appropriate for NAC; the C-O distance and the O-C-F angle are reasonable for the S(N) 2 reaction. The activation energy is greatly reduced in this conformation because of three hydrogen bonds between the leaving F atom and surrounding amino acid residues. Chloroacetate cannot reach the reactive conformation, due to the longer C-Cl bond; this results in an increase of the activation energy despite the weaker C-Cl bond. PMID:22674735

Mixed ionic-electronic conducting perovskite type oxides with a general formula ABO(3) (where A = Ba, Sr, Ca and B = Co, Fe, Mn) often have high mobility of the oxygen vacancies and exhibit strong ionic conductivity. They are key materials that find use in several energy related applications, including solid oxide fuel cell (SOFC), sensors, oxygen separation membranes, and catalysts. Barium/strontium cobaltite/ferrite (BSCF) Ba(0.5)Sr(0.5)Co(0.8)Fe(0.2)O(3-delta) was recently identified as a promising candidate for cathode material in intermediate temperature SOFCs. In this work, we perform experimental and theoretical study of the local atomic structure of BSFC. Micro-Raman spectroscopy was performed to characterize the vibrational properties of BSCF. The Jahn-Teller distortion of octahedral coordination around Co(4+) cations was observed experimentally and explained theoretically. Different cations and oxygen vacancies ordering are examined using plane wave pseudopotential density functional theory. We find that cations are completely disordered, whereas oxygen vacancies exhibit a strong trend for aggregation in L-shaped trimer and square tetramer structure. On the basis of our results, we suggest a new explanation for BSCF phase stability. Instead of linear vacancy ordering, which must take place before the phase transition into brownmillerite structure, the oxygen vacancies in BSCF prefer to form the finite clusters and preserve the disordered cubic structure. This structural feature could be found only in the first-principles simulations and can not be explained by the effect of the ionic radii alone. PMID:20355954

Theoretical investigation of guanine, DNA base adsorption on the ZnO model clusters, viz., Zn2O2, Zn3O3, Zn4O4 ring (R) and Zn4O4 wurtzite (W) in terms of geometry, binding site, binding energy (EB), energy gap (Eg), electronic and spectral properties were studied by a density functional theory (DFT) method. The guanine adsorption on the ZnO (G-ZnO) clusters is modeled by the B3LYP/LanL2DZ method. The calculated binding energy (EB) and energy gap (Eg) of the guanine molecule are highly dependent on the nature of the cluster size and vary with the size of the clusters. Physisorption proceeded via formation of the NZn bond between guanine and the active Zn(2+) site on ZnO. The HOMO-LUMO energies show that charge transfer occurs in the G-ZnO clusters, from ZnO to guanine to better understand the interaction. The Mulliken charges are computed. The electronic properties of ZnO and G-ZnO clusters were compared with different basis sets (B3LYP/6-31G, B3LYP/6-311G, MP2/6-31G and MP2/LanL2DZ). Experimental information like microscopic and spectroscopic evidence is also included for understanding the guanine-ZnO interactions. The G-ZnO composite was prepared by a precipitation method and characterized by SEM with EDX, FT-IR and FT-RAMAN analysis. The interaction of guanine with ZnO nanoparticles was observed by UV-vis spectroscopy. The experimental results are compared with the DFT results in the light of these new insights. PMID:25266048

The first-principles calculations were applied to investigate the thermo-physical properties of Ca{sub 3}Si{sub 4} compound with increasing pressure. Those properties are based on density functional theory (DFT) method within the generalized gradient approximation (GGA) and local density approximation (LDA) for exchange and correlation. The optimized lattice constant and formation enthalpy are in good agreement with the experimental data and other theoretical data available. The calculated band structures confirm that Ca{sub 3}Si{sub 4} is a semiconductor with an indirect band gap of 0.363 eV (GGA) and 0.311 eV (LDA) at 0 GPa, and the calculated band gap decreased with the increasing pressure. The elastic constants, elastic anisotropy, elastic moduli and Poisson's ratio of Ca{sub 3}Si{sub 4} have also been obtained under high pressures. The Debye temperature, heat capacity, coefficient of thermal expansion and Grueneisen parameter have also been calculated in the quasiharmonic Debye model. - Graphical abstract: The Partial Density of States and Band Structure of Ca{sub 3}Si{sub 4}. Highlights: Black-Right-Pointing-Pointer The thermo-physical properties of Ca{sub 3}Si{sub 4} have been investigated. Black-Right-Pointing-Pointer Ca{sub 3}Si{sub 4} is a semiconductor with an indirect band gap. Black-Right-Pointing-Pointer The mechanical properties of Ca{sub 3}Si{sub 4} have been studied. Black-Right-Pointing-Pointer The heat capacity and thermal expansion have been obtained.

An important problem, that has to be solved before hydrogen shall become a fuel for commercial applications, is the choice of a suitable storage media. It has been proposed that the incorporation of porous materials in a gas tank could lead to an increase of the gas amount stored in the tank with safety. Recently, new families of porous materials, such as Metal-Organic Frameworks (MOF) and Covalent-Organic Frameworks (COF) has been proposed for hydrogen storage application due to their ability to absorb large amounts of hydrogen. Materials that can be suitable for hydrogen storage should meet some requirements, such as high surface area, high pore volume, chemical and thermal stability and increased energetic interactions with the hydrogen. Many MOF and some COF materials have achieved to capture big amounts of hydrogen in their structures, which has been attributed to the some of the above mentioned properties. The investigation of the interaction of hydrogen with the host materials is a crucial step for the better understanding of the storage properties of those materials and for the further enhance of their storage abilities.

The mechanism of lithium intercalation/deintercalation for phase Al0.8Ni3Sn0.2 as anode material used in lithium ion battery was studied carefully based on the first-principle plane wave pseudo-potential method. The calculated results indicated that Sn-Ni-Al alloy had high theoretical capacity when used as anode material, however, there was high initial irreversible capacity loss because of the large volume expansion. Therefore the technological parameters during preparing the Sn-Ni-Al anode should be controlled strictly to make the content of Al0.8Ni3Sn0.2 phase as low as possible and to make the anode consist of promising Sn-Ni and Al-Ni phases. For comparison, an experiment based on magnetron sputtering was done. The result showed that the calculation is in good agreement with the experiment. We found that the first-principle investigation method is of far-reaching significance in synthesising new commercial anode materials with high capacity and good cycle performance.

Tungsten trioxide WO3 is an interesting semiconductor with a wide-range of potential applications. One important property of WO 3 is its electrochromic behavior, which has generated significant research interest. Electrochromic materials exhibit reversible and persistent changes of the optical properties, hence their color, upon applying an electrical pulse. The applications of the electrochromic WO3 range from information display, light shutters, to energy efficient smart windows. Although there are many materials that exhibit electrochromic behavior, tungsten trioxide is one of the most extensively studied ones due to its superior coloration efficiency, short response time and reversibility. Enhanced electrochromic properties in WO3 nanowires have been reported recently. Despite much research effort, a first-principles theory for the coloration mechanism in this material has not emerged. In this work, we establish a first-principles theory for the coloration mechanism in NaxWOx, which is also able to explain the electrochromism in WO3. Chapter 1 gives a brief introduction to electrochromism in WO3 and related materials. In Chapter 2, we summarize the theories and computational methods used in this work including the local density approximation (LDA) within density functional theory (DFT), pseudopotential planewave formalism and the GW approximation. We study the crystal and electronic structures of WO3 in Chapter 3. WO3 has a basic octahedron structure. From -140 ˜ 830°C, the crystal structure changes from monoclinic to triclinic, again monoclicnic, then successively orthorhombic, tetragonal, and again tetragonal. Several groups have investigated the electronic structure of WO3 within DFT, but the band gap is severely underestimated compared with experiment. We have carried out quasiparticle calculations within the GW approximation. The calculated band gap is much closer to experimental results. Chapter 4 and Chapter 5 discuss the optical properties and coloration mechanism of WO3 upon charge insertion. The calculated dielectric functions, reflectance, transmission and absorption coefficient agree very well with experiments. Our results explain the systematic change in color of Na3WO3 from blue to golden-yellow with increasing sodium concentration x. We find that proper accounts for the free-carriers contribution to the optical response are critical for a quantitative understanding of the coloration mechanism in this system. Besides WO3, we have studied another "smart material", VO2. The results are reported in chapter 6. The most interesting property of VO2 is its metal-insulator transition (MIT) at T c=340 K. The crystal structure changes from a high-temperature rutile phase to a low-temperature monoclinic phase at Tc. The MIT in VO2 has led to many practical applications such as thermocoatings, optical switching devices etc. However, it has long been a controversial issue regarding the mechanism behind the MIT. It is still not clear whether the insulating behavior is driven by the electron correlation or structural distortions. In this work, we perform first-principles electronic structure calculation using both LDA and LDAU method. It is found that the correlation effect is very important to explain the insulating phase of VO2. However, correlation effects alone cannot help open a band gap for the insulating phase of VO2. Structural distortion also plays an important role. It seems that it is the subtle interplay between the electron-electron correlation and electron-lattice interaction that ultimately drives the development of an insulating gap.

Conspectus Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from firstprinciples. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from firstprinciples, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be extrapolated to such cases. As an alternative to applying SAPT(DFT) in crystal structure calculations, one can use supermolecular DFT interaction energies combined with scaled dispersion energies computed from simple atom-atom functions, that is, use the so-called DFT+D approach. Whereas the standard DFT methods fail for intermolecular interactions, DFT+D performs reasonably well since the dispersion correction is used not only to provide the missing dispersion contribution but also to fix other deficiencies of DFT. The latter cancellation of errors is unphysical and can be avoided by applying the so-called dispersionless density functional, dlDF. In this case, the dispersion energies are added without any scaling. The dlDF+D method is also one of the best performing DFT+D methods. The SAPT(DFT)-based approach has been applied so far only to crystals with rigid monomers. It can be extended to partly flexible monomers, that is, to monomers with only a few internal coordinates allowed to vary. However, the costs will increase relative to rigid monomer cases since the number of grid points increases exponentially with the number of dimensions. One way around this problem is to construct force fields with approximate couplings between inter- and intramonomer degrees of freedom. Another way is to calculate interaction energies (and possibly forces) "on the fly", i.e., in each step of lattice energy minimization procedure. Such an approach would be prohibitively expensive if it replaced analytic force fields at all stages of the crystal predictions procedure, but it can be used to optimize a few dozen candidate structures determined by other methods. PMID:25354310

We developed a first-principles approach based on nonequilibrium Green's function (NEGF) combined with density functional theory (DFT) to investigate quantum transport properties of normal-metal-superconductor (N-S) hybrid systems. As an application of our theory, we investigated the Andreev conductance of atomic wires consisting of 4-15 carbon atoms in contact with one normal Al lead and another superconducting Al lead from firstprinciples. Numerical results show that the Andreev conductance oscillates between an even and odd number of carbon atoms. In the presence of the superconducting lead, the self-consistent scattering potential of the N-S system can be very different from that of the corresponding normal system. Furthermore, a small change of scattering potential can give rise to a significant change of Andreev conductance. For an even number of carbon atoms, the change of scattering potential gives rise to a 4-7% difference in conductance, while when the number of carbon atoms n is odd, a 14-30% change of conductance is observed due to the potential change. We find that the charge transfer plays an important role in N-S systems. For the carbon wire with normal Al contacts, there is a significant charge transfer in real space that is responsible for the even-odd oscillation in conductance. When a superconducting lead is present, the charge is redistributed in momentum space, although it is almost not changed in real space. For even n, a 10% change of charge density at Fermi level is found mainly in the lead region. For odd n, however, the change of charge density at Fermi level is even more than 30% near the first, third, etc., carbon atoms. Since less charge density is available at Fermi level, there is a decrease in conductance for all carbon wires, especially for the wires with odd number of carbon atoms. Our results indicate that the self-consistent calculation of the scattering potential is necessary to obtain an accurate Andreev conductance of N-S hybrid structures.

Using dynamic force spectroscopy to measure the kinetic off-rates of intermolecular bonds currently requires the isolation of single molecules. This requirement arises in part because no tractable analytic method for determining kinetic off-rates from the rupture of a large number of bonds under dynamic forces is currently available. We introduce a novel method for determining the unstressed off-rate from dynamic force spectroscopy experiments involving a large number of bonds. Using both the Bell and Dembo models we show that the unstressed off-rate calculated using the proposed method is in good agreement with the prescribed unstressed off-rate used in Monte-Carlo simulations of multiple bond dynamic force spectroscopy experiments given initial number of bonds (50–500) and loading rate 103 – 106 pN/s. PMID:22417406

First-principles calculations based on density functional theory have been performed for the quaternary GaAs1- x- y N x Bi y alloy lattice-matched to GaAs. Using the state-of-the-art computational method with the Heyd-Scuseria-Ernzerhof (HSE) hybrid functional, electronic, and optical properties were obtained, including band structures, density of states (DOSs), dielectric function, absorption coefficient, refractive index, energy loss function, and reflectivity. It is found that the lattice constant of GaAs1- x- y N x Bi y alloy with y/ x =1.718 can match to GaAs. With the incorporation of N and Bi into GaAs, the band gap of GaAs1- x- y N x Bi y becomes small and remains direct. The calculated optical properties indicate that GaAs1- x- y N x Bi y has higher optical efficiency as it has less energy loss than GaAs. In addition, it is also found that the electronic and optical properties of GaAs1- x- y N x Bi y alloy can be further controlled by tuning the N and Bi compositions in this alloy. These results suggest promising applications of GaAs1- x- y N x Bi y quaternary alloys in optoelectronic devices.

We study the structural stability of the singly and doubly charged (positively and negatively) Si-doped heterofullerene C30Si30 via density-functional theory calculations combined with first-principles molecular dynamics. Geometry optimization aimed at establishing the most stable configurations at T=0K shows that C30Si30 undergoes very limited changes in the bond lengths after addition or extraction of one or two electrons. Consideration of thermal motion reveals that the dynamical stability is not significantly altered in C30Si30- with respect to the neutral case. On the contrary, Si-Si and C-C bond stretching followed by rapid fragmentation, occurring in less than 1 ps, are observed for C30Si30-- . This effect is encountered in two sets of calculations performed with the periodic cell and the isolated cell boundary conditions for the heterofullerene. In the periodic case, fragmentation is due to the predominance of Si atoms carrying charges of equal sign in the Si-rich portion of the cage. In the isolated case, the number of neighboring charges of equal sign is reduced but the strength of the residual repulsive interaction is sufficient to destabilize the network at finite temperature. The lack of stability of doubly charged Si-doped heterofullerenes confirms that the observed charged species are the singly charged ones.

Despite the increasing importance of ruthenium in numerous technological applications, e.g., catalysis and electronic devices, experimental and computational data on its binary alloys are sparse. In particular, data are scant on those binary systems believed to be phase-separating. We performed a comprehensive study of ruthenium binary systems with the 28 transition metals, using high-throughput first-principles calculations. These computations predict novel unsuspected compounds in 7 of the 16 binary systems previously believed to be phase-separating and in two of the three systems reported with only a high-temperature ? phase. They also predict a few unreported compounds in five additional systems and indicate that some reported compounds may actually be unstable at low temperature. These new compounds may be useful in the rational design of new Ru-based catalysts. The following systems are investigated: AgRu, AuRu, CdRu, CoRu, CrRu, CuRu, FeRu, HfRu, HgRu, IrRu, MnRu, MoRu, NbRu, NiRu, OsRu, PdRu, PtRu, ReRu, RhRu, RuSc, RuTa, RuTc, RuTi, RuV, RuW, RuY, RuZn, and RuZr (a star denotes systems in which the ab initio method predicts that no compounds are stable).

A first-principles study of phase stability of various phases of Ti2N under normal conditions and as a function of pressure was carried out. Among the ? and ?'phases of Ti2N that are observed experimentally, ?-Ti2N is the most stable. The ?' phase can only exist at high temperature due to the soft acoustic modes at the X point. The origin of the tetragonal structure of both the ? and ?' phases is supposed to be caused by the tetragonal local lattice distortion around a nitrogen vacancy. Based on the results of the total-energy and phonon-spectrum calculations at zero temperature, the following sequence of phase transformation in Ti2N under pressure is predicted: ?-Ti2N (space group P4/mnm), P = 77.5 GPa ? Au2Te type (space group C2/m), P = 86.7 GPa ? Al2Cu type (space group I4/mcm). The present study shows that, to correctly predict relative phase stability, the peculiarities of the phonon spectra of the materials under investigation have to be properly accounted for.

The semiconducting single-walled carbon nanotube (C-SWNT) has been synthesized by S-doping, and they have extensive potential application in electronic devices. We investigated the electronic structures of S-doped capped (5, 5) C-SWNT with different doping position using firstprinciples calculations. It is found that the electronic structures influence strongly on the workfunction without and with external electric field. It is considered that the extended wave functions at the sidewall of the tube favor for the emission properties. With the S-doping into the C-SWNT, the HOMO and LUMO charges distribution is mainly more localized at the sidewall of the tube and the presence of the unsaturated dangling bond, which are believed to enhance workfunction. When external electric field is applied, the coupled states with mixture of localized and extended states are presented at the cap, which provide the lower workfunction. In addition, the wave functions close to the cap have flowed to the cap as coupled states and to the sidewall of the tube mainly as extended states, which results in the larger workfunction. It is concluded that the S-doped C-SWNT is not incentive to be applied in field emitter fabrication. The results are also helpful to understand and interpret the application in other electronic devices. PMID:20672070

Realization of controlled binary switching in individual molecules is of fundamental importance for nanoscale electronics where the use of molecular components promises the flexibility of engineering performance through controlled organic synthesis. The active component of the [2]rotaxane molecule consists of a cyclobis-(paraquat-p-phenylene) ring-shaped structure [(CBPQT(4+))(PF(6)(-))(4)], proposed to switch between two stations, tetrathiafulvalene (TTF) and 1,5-dioxynapthalene (DNP), that lie along a common molecular backbone. However, there are still several open questions regarding their operation and performance, particularly in a device geometry. In this work, the switching speed of crossbar array devices based on [2]rotaxane arrays is studied with firstprinciples density functional theory (DFT). The energetics of a likely configurational pathway for the CBPQT-ring shuttling along the molecular backbone between stations is computed and analyzed, as are ionization potentials and electrostatic screening properties. From these quantities, a new switching mechanism is identified. The applied bias at the cathode alters the energy landscape, making the OFF-state configuration energetically unfavorable relative to the ON-state without involving charging, as previously suggested. (1) For a crossbar memory array of reasonable size, the calculations predict that the switching speed is dominated by the shuttling time of the CBPQT-ring, which is estimated to be a few microseconds. The applicability of this technology is discussed in light of this result. PMID:19705804

While yttrium and impurity segregation at interfaces of yttria-stabilized zirconia (YSZ) has been intensively studied experimentally, the mechanisms governing the propensity for segregation are still not fully understood. The segregation energetics of yttrium and aluminum, another common segregant at interfaces of YSZ, were studied by means of firstprinciples calculations based on density functional theory. Site-dependent formation energies were calculated following the substitutional incorporation of yttrium and aluminum in the near-interface region of the ?5(310) grain boundary in cubic zirconia, for which recent experimental data revealed strong yttrium enrichment. Aluminum segregation was found to be strongly favored, accompanied by extensive changes in its local environment and coordination. Yttrium displayed a segregation propensity dependent on the site of substitution that correlated with the ability of its surrounding environment to accommodate the misfit strain by a breathing-type relaxation and increase of the nearest-neighbor yttrium-oxygen distances. Formation energies of oxygen vacancies were also determined near the interface, both as isolated defects and also by considering cosegregation with yttrium; the ensuing defect association led to stable yttrium-vacancy complexes and increased the energy gain from yttrium incorporation at the core of the grain boundary.

First-principles calculations are performed for Mg2+ and Zn2+ substitution in hydroxyapatite (HAp) and octacalcium phosphate (OCP), because the foreign ions are known to play an important role for bone formation. In order to study their possible location in the system of HAp in contact with the aqueous solution, OCP is considered as a structural model of the transition region between HAp and the solution. It is found that, when the foreign ions substitute for Ca sites, the surrounding oxygen ions undergo considerable inward relaxation, due to their smaller ionic sizes than Ca2+, which results in the smaller coordination numbers with oxygen as compared with those of Ca in bulk HAp and OCP. From the calculated defect formation energies, it is likely that the substitutional foreign ions are quite difficult to dissolve into HAp whereas can be more easily incorporated in OCP. In particular, Zn2+ can more favorably substitute for the specific Ca site of OCP, as compared to Mg2+, which is attributed with covalent bond formation between Zn and the surrounding oxygen ions. It is thus considered that zinc may play its role to promote bone formation by being incorporated into the transition region between HAp and the surrounding solution.

The elasticity, dynamic properties, and superconductivity of {alpha}, {omega}, and {beta} Zr upon compression are investigated by using first-principles methods. Our calculated elastic constants, elastic moduli, and Debye temperatures of {alpha} and {omega} phases are in excellent agreement with experiments. Electron-phonon coupling constant {lambda} and electronic density of states at the Fermi level N (E{sub F}) are found to increase with pressure for these two hexagonal structures. For cubic {beta} phase, the critical pressure for mechanical stability is predicted to be 3.13 GPa and at P = 4 GPa the low elastic modulus (E=31.97 GPa) can be obtained. Besides, the critical pressure for dynamic stability of {beta} phase is achieved by phonon dispersion calculations to be {approx}26 GPa. Over this pressure, {lambda} and N (E{sub F}) of {beta} phase decrease upon further compression. Our calculations show that the large value of superconducting transition temperature T{sub c} at 30 GPa for {beta} Zr is mainly due to the TA1 soft mode. Under further compression, the soft vibrational mode will gradually fade away.

Using first-principles method within the framework of the density functional theory, we study the influence of native point defect on the structural and electronic properties of Bi2Se3. Se vacancy in Bi2Se3 is a double donor, and Bi vacancy is a triple acceptor. Se antisite (SeBi) is always an active donor in the system because its donor level (?(+1/0)) enters into the conduction band. Interestingly, Bi antisite (BiSe1) in Bi2Se3 is an amphoteric dopant, acting as a donor when ?e < 0.119 eV (the material is typical p-type) and as an acceptor when ?e > 0.251 eV (the material is typical n-type). The formation energies under different growth environments (such as Bi-rich or Se-rich) indicate that under Se-rich condition, SeBi is the most stable native defect independent of electron chemical potential ?e. Under Bi-rich condition, Se vacancy is the most stable native defect except for under the growth window as ?e > 0.262 eV (the material is typical n-type) and ??Se < -0.459 eV (Bi-rich), under such growth window BiSe1 carrying one negative charge is the most stable one.

We investigate the structural and electronic properties and formation energies of vacancy, interstitial, and antisite defects, as well as complex formation, in wurtzite InN using first-principles calculations. The N interstitial, which forms a split-interstitial configuration with a N2 -like bonding, has the lowest formation energy under N-rich conditions in p -type material, where it is a triple donor. We find that indium vacancies have a tendency to form “clusters,” which results in local nitrogen-rich regions and the formation of Nx -molecular-like bonds. These complexes are amphoteric, have a relatively high formation energy, and are formed more readily under N-rich conditions. The nitrogen vacancy is a low energy defect under more In-rich conditions, and in p -type material it acts as a single and triple donor. In the neutral and negative charge states, we find nitrogen vacancies also prefer to be situated close to one another and to cluster, giving rise to local In-rich regions with electron localization at these metalliclike bonding configurations. The indium antisite in the 4+ charge state is the lowest-energy defect under In-rich conditions in p -type material and thus also acts as a donor. Our findings shed light on, and help explain, recent and sometimes conflicting, experimental observations.

We present the first-principles calculations of vibrational and thermal properties for wurtzite and zinc-blende zinc oxide (ZnO) within DFT and quasi-harmonic approximation, especially for their negative thermal expansion (NTE) behavior. For the wurtzite and zinc-blende phases, negative thermal expansions are obtained at T < 95 K and T < 84 K, respectively. For the wurtzite structure, calculated phonon frequencies and mode Grüneisen parameters of low-energy modes are in good agreement with that determined experimentally. And the thermal expansion coefficient is found to be in good agreement with the experimental results. Like many other NTE semiconductors, detailed study of both phases shows that maximum contribution to NTE comes from low-frequency transverse acoustic modes, while for the wurtzite structure the contribution of longitudinal acoustic and lowest-energy optical modes is not ignorable. From the specific analysis of the vibration modes, we found that the negative thermal expansion in ZnO is dominated by the tension effect.

Some highly ordered compounds of graphene oxide (GO), e.g., the so-called clamped and unzipped GO, are shown to have piezoelectric responses via first-principles density functional calculations. By applying an electric field perpendicular to the GO basal plane, the largest value of in-plane strain and strain piezoelectric coefficient, d31 are found to be 0.12% and 0.24 pm/V, respectively, which are comparable with those of some advanced piezoelectric materials. An in-depth molecular structural analysis reveals that the deformation of the oxygen doping regions in the clamped GO dominates its overall strain output, whereas the deformation of the regions without oxygen dopant in the unzipped GO determines its overall piezoelectric strain. This understanding explains the observed dependence of d31 on oxygen doping rate, i.e., higher oxygen concentration giving rise to a larger d31 in the clamped GO whereas leading to a reduced d31 in the unzipped GO. As the thinnest two-dimensional piezoelectric materials, GO has a great potential for a wide range of micro/nano-electromechanical system (MEMS/NEMS) actuators and sensors.

The surface chemical activity is a critical factor affecting the photocatalytic efficiency of hematite. In this study, we investigate systematically the reaction kinetics of water heterolytic dissociation (H2O-OH(-) + H(+)) and hydrogen generation by water splitting on four kinds of hematite (0001) surfaces, namely perfect and defective O- and Fe-terminated surfaces, at the electronic level based on first-principles calculations. The simulation results illustrate that the chemical reaction rate for the dissociation and hydrogen generation is sensitive to the morphology of the hematite (0001) surface. For water heterolytic dissociation, the hydrogen atom is apt to drop from water molecules on the perfect O-terminated (0001) surface without energy consumption. However, the Fe-terminated (0001) perfect surface is a preferable candidate for hydrogen generation, on which the whole photoelectrochemical process needs to overcome a rate determined barrier of 2.77 eV. Our investigation shows that O- or Fe-vacancy on hematite (0001) surfaces is not conductive to hydrogen generation by water splitting. PMID:25342277

Al-Mg-Si-(Cu) alloys form the basis of a wide variety of commercial precipitation-hardened alloys, and the observed precipitation sequence in these alloys is complex and involves a wide variety of metastable phases (e.g. GP zones, {beta}'', U1, U2, B{sup '}, {beta}{sup '}). Calculations of metastable phase equilibria in these alloys are virtually nonexistent due to the lack of quantitative information on the thermodynamics of the precipitate phases. We have undertaken an extensive, systematic first-principles study of energetics of all the reported precipitate phases of Al-Mg-Si-(Cu) alloys, using density functional-based calculations in both the local density and generalized gradient approximations. Our calculations help clarify the energetics of the metastable precipitate phases, and in certain cases, provide insight into the compositional changes of precipitates during aging. In addition to energetics, we also examine the relative volumes of the various phases, and discuss cases of significant deviation from that of the solid solution.

While metallic fuels have a long history of reactor use, their fundamental physical and thermodynamic properties are not well understood. Many metallic nuclear fuels are body-centered cubic alloys of uranium that swell under fission conditions, creating fission product gases such as helium, xenon and krypton. In this paper, helium, xenon, and krypton point defects are investigated in the ? and ? phases of metallic uranium using firstprinciples calculations. A density functional theory (DFT) framework is utilized with projector augmented-wave (PAW) pseudopotentials. Formation and incorporation energies of He, Xe, and Kr are calculated at various defect positions for the prediction of fission gas behavior in uranium. In most cases, defect energies follow a size effect, with helium incorporation and formation energies being the smallest. The most likely position for the larger Xe and Kr atoms in uranium is the substitutional site. Helium atoms are likely to be found in a wide variety of defect positions due to the comparable formation energies of all defect configurations analyzed. This is the first detailed study of the stability and incorporation of fission gases in uranium.

The positions of electronic band edges are one important metric for determining a material's capability to function in a solar energy conversion device that produces fuels from sunlight. In particular, the position of the valence band maximum (conduction band minimum) must lie lower (higher) in energy than the oxidation (reduction) reaction free energy in order for these reactions to be thermodynamically favorable. We present firstprinciples quantum mechanics calculations of the band edge positions in five transition metal oxides and discuss the feasibility of using these materials in photoelectrochemical cells that produce fuels, including hydrogen, methane, methanol, and formic acid. The band gap center is determined within the framework of DFT+U theory. The valence band maximum (conduction band minimum) is found by subtracting (adding) half of the quasiparticle gap obtained from a non-self-consistent GW calculation. The calculations are validated against experimental data where possible; results for several materials including manganese(ii) oxide, iron(ii) oxide, iron(iii) oxide, copper(i) oxide and nickel(ii) oxide are presented. PMID:21853210

Thermodynamic calculations that combine experimental data with the results of firstprinciples calculations yield negative free energies for {1 1 1} surfaces of nickel ferrite for the temperature, pressure and ion concentrations typical of Pressurized Light Water Reactor (PWR) coolant. When combined with a positive bulk free energy of formation, the negative surface energies predict that thermodynamically-stable octahedral nickel ferrite particles with diameters of ?50 nm should be present in PWR coolant during operation. These particles would not be removed by mixed bed demineralizers and would be below the filter pore sizes typically used in Chemical and Volume Control Systems. The calculations also predict that these particles are not thermodynamically stable in coolant under ambient conditions. Based on these results it is proposed that solvated nickel ferrite particles, which are predicted to be stable and likely long-lived in PWR primary coolant, contribute to the nucleation of metal oxide scale on PWR fuel rod cladding and that conventional methods for purifying the primary coolant may be ineffective in removing these species.

Efficient Monte Carlo algorithms are combined with the Quickstep energy routines of CP2K to develop a program that allows for Monte Carlo simulations in the canonical, isobaric-isothermal, and Gibbs ensembles using a firstprinciples description of the physical system. Configurational-bias Monte Carlo techniques and pre-biasing using an inexpensive approximate potential are employed to increase the sampling efficiency and to reduce the frequency of expensive ab initio energy evaluations. The new Monte Carlo program has been validated through extensive comparison with molecular dynamics simulations using the programs CPMD and CP2K. Preliminary results for the vapor-liquid coexistence properties (T = 473 K) of water using the Becke-Lee-Yang-Parr exchange and correlation energy functionals, a triple-zeta valence basis set augmented with two sets of d-type or p-type polarization functions, and Goedecker-Teter-Hutter pseudopotentials are presented. The preliminary results indicate that this description of water leads to an underestimation of the saturated liquid density and heat of vaporization and, correspondingly, an overestimation of the saturated vapor pressure.

We report on the aqueous hydration of benzene and hexafluorobenzene, as obtained by carrying out extensive (>100 ps) firstprinciples molecular dynamics simulations. Our results show that benzene and hexafluorobenzene do not behave as ordinary hydrophobic solutes, but rather present two distinct regions, one equatorial and the other axial, that exhibit different solvation properties. While in both cases the equatorial regions behave as typical hydrophobic solutes, the solvation properties of the axial regions depend strongly on the nature of the {pi}-water interaction. In particular, {pi}-hydrogen and {pi}-lone pair interactions are found to dominate in benzene and hexafluorobenzene, respectively, which leads to substantially different orientations of water near the two solutes. We present atomic and electronic structure results (in terms of Maximally Localized Wannier Functions) providing a microscopic description of benzene- and hexafluorobenzene-water interfaces, as well as a comparative study of the two solutes. Our results point at the importance of an accurate description of interfacial water in order to characterize hydration properties of apolar molecules, as these are strongly influenced by subtle charge rearrangements and dipole moment redistributions in interfacial regions.

We report the investigation of electron tunneling mechanism of peptide ferrocenyl-glycylcystamine self-assembled monolayers (SAMs) onto Au (111) electrode surfaces. Recent experimental investigations showed that electron transfer in peptides can occur across long distances by separating the donor from the acceptor. This mechanism can be further fostered by the presence of electron donor terminations of Fc terminal units on SAMs but the charge transfer mechanism is still not clear. We study the interaction of the peptide ferrocenyl-glycylcystamine on the Au (111) from firstprinciples calculations to evaluate the electron transfer mechanism. For this purpose, we used the Kohn Sham (KS) scheme for the Density Functional Theory (DFT) as implemented in the Quantum-ESPRESSO suit of codes, using Vandebilt ultrasoft pseudopotentials and GGA-PBE exchange correlation functional to evaluate the ground-state atomic and electronic structure of the system. The analysis of KS orbital at the Fermi Energy showed high electronic density localized in Fc molecules and the observation of a minor contribution from the solvent and counter ion. Based on the results, we infer evidences of electron tunneling mechanism from the molecule to the Au(111).

We present first-principles calculations of the formation energy of different native defects and their complexes in wurtzite InN using density-functional theory and the pseudopotential plane-wave method. Our calculations are aimed in the three cases: N/In = 1, N/In > 1 (N-rich), and N/In < 1 (In-rich). Our results indicate that the antisite defect has the lowest formation energy under N/In = 1. The formation energy of nitrogen interstitial (nitrogen vacancy) defect is significantly low under the N-rich (In-rich) condition. Thus the antisite defect is an important defect if N/In = 1, and the nitrogen interstitial (nitrogen vacancy) defect is a vital defect under the N-rich (In-rich) condition. The atomic site relaxation around the nitrogen interstitial and vacancy is investigated. Our calculations show that the nitrogen vacancy cannot be observed although it is one of the most important defects in InN. Our results are confirmed by experiments.

Performance of the ITER is anticipated to be highly sensitive to the edge plasma condition. The edge pedestal in ITER needs to be predicted from an integrated simulation of the necessary first-principles, multi-scale physics codes. The mission of the SciDAC Fusion Simulation Project (FSP) Prototype Center for Plasma Edge Simulation (CPES) is to deliver such a code integration framework by (1) building new kinetic codes XGC0 and XGC1, which can simulate the edge pedestal buildup; (2) using and improving the existing MHD codes ELITE, M3D-OMP, M3D-MPP and NIMROD, for study of large-scale edge instabilities called Edge Localized Modes (ELMs); and (3) integrating the codes into a framework using cutting-edge computer science technology. Collaborative effort among physics, computer science, and applied mathematics within CPES has created the first working version of the End-to-end Framework for Fusion Integrated Simulation (EFFIS), which can be used to study the pedestal-ELM cycles.

GaFeO3 (GFO) is a room temperature piezoelectric material with antiferromagnetic ordering in the ground state. However, experimental observation reports ferrimagetic behavior below the magnetic transition temperature, attributed to the site disorder of Fe and Ga sites. This transition occurs at temperatures close to room temperature, depending upon the Fe content of the material. Previous structural characterization studies indicate that the room temperature crystal structure (Pc21n) is retained at least until 4 K. While there are a few experimental studies on this compound, there is no well established understanding of its electronic structure and lattice dynamics which can give insight into the piezoelectric and magnetic properties of the material. From this perspective, we started our calculations with the experimental lattice parameters of stoichiometric GFO assuming no partial occupancies of the constituent ions. The calculations are carried out using local spin density approximation (LSDA+U). Electronic structure and Born effective charges were calculated based on the ground state structure. Firstprinciples density functional theory based calculations using small displacement method was adopted to calculate the phonon dispersion relations for the material. On the basis of the dispersion relations modes were assigned.

The first-principles density functional calculation is used to investigate the electronic structures and magnetic properties of Mn-doped and N-co-doped ZnO nanofilms. The band structure calculation shows that the band gaps of ZnO films with 2, 4, and 6 layers are larger than the band gap of the bulk with wurtzite structure and decrease with the increase of film thickness. However, the four-layer ZnO nanofilms exhibit ferromagnetic phases for Mn concentrations less than 24% and 12% for Mn-doping performed in the whole layers and two layers of the film respectively, while they exhibit spin glass phases for higher Mn concentrations. It is also found, on the one hand, that the spin glass phase turns into the ferromagnetic one, with the substitution of nitrogen atoms for oxygen atoms, for nitrogen concentrations higher than 16% and 5% for Mn-doping performed in the whole layers and two layers of the film respectively. On the other hand, the spin-glass state is more stable for ZnO bulk containing 5% of Mn impurities, while the ferromagnetic phase is stable by introducing the p-type carriers into the bulk system. Moreover, it is shown that using the effective field theory for ferromagnetic system, the Curie temperature is close to the room temperature for the undamped Ruderman—Kittel—Kasuya—Yoshida (RKKY) interaction.

Li7P3S11 has been shown to be a promising superionic conductor for solid state rechargeable batteries with a room temperature conductivity as high as 10-3 S/cm and a thermal activation energy as small as EA=0.12 eV.ootnotetext F. Mizuno et al., Solid State Ionics 177, 2721 (2006). We have performed firstprinciples modeling studiesootnotetextN. A. W. Holzwarth, N. D. Lepley, Y. A. Du, J. Power Sources 196, 6870 (2011). on this material in order to explain its stability and Li ion migration properties. Our investigation considers optimized crystal structures, migration involving both vacancy and interstitial mechanisms, as well as related materials. We find optimized crystal structures in reasonable agreement with experiment,ootnotetextH. Yamane et al., Solid State Ionics 178, 1162 (2007); Y. Onodera et al., J. Phys. Soc. Jpn. 79, 87 (2010), suppl. A. and the lowest calculated activation energy barrier was found to be EA=0.15 eV in good agreement with the experimental value.